Lab Faqs

Great information compact format the RAS Lab FAQS, 3rd edition
Dear Valued Customer,

At Roche Applied Science, we know that time is an increasingly scarce resource these days. Relevant information, available at your fingertips at the right time and in an easily accessible format can help you perform your experiments more efficiently. Based upon requests from many different customers, Roche Applied Science has updated Lab FAQS. We hope you find this new compendium of information even more useful for your laboratory work. Think of the Lab FAQS as our way of saying Thank you for using our reagents, kits and systems over the years. We wish you continued success in your research projects. Sincerely Roche Applied Science
PS: To offer comments and/or suggestions on content, structure and/or layout of this guide, please dont hesitate to contact Bettina Kruchen (e-mail: Bettina.Kruchen@roche.com) or your local representative. Your cooperation in improving Lab FAQs is highly appreciated.
Acknowledgements:
We thank all contributors and editors for their diligent efforts during the proofreading and production of this book. Without their help, this project would never have been realized.
Editorial management 3rd edition: Doris Eisel, Design and Layout Urs W. Hoffmann-Rohrer, DKFZ , Heidelberg, Editor in Chief Bettina Kruchen, Editor in Chief Paul Labaere, Scientific Advice Stefanie Gruenewald-Janho, Scientific Advice Oliver Seth, Scientific Advice Michael Hoffmann, Scientific Advice Doris Schmitt, Scientific Advice Jasmina Putnik, Scientific Advice Gudrun Tellmann, Scientific Advice Hans-Jrgen Rode, Scientific Advice Rita Rein, Scientific Advice Simone Pitz, Scientific Advice Brigitte Hloch, Scientific Advice Critical reading of the manuscript: Yair Argon, University of Chicago, USA Hans-Joachim Degen, RAS, Germany Ingrid Hoffmann, DKFZ, Heidelberg, Germany Jrgen Kartenbeck, DKFZ, Heidelberg, Germany Bernhard Korn, RZPD, Berlin/Heidelberg, Germany Annette Moritz, RAS, Germany Sabine Muench-Garthoff, RAS, Germany Attila Nemeth, University of Budapest, Hungary Hanspeter Pircher, University of Freiburg, Germany Herwig Ponstingel, DKFZ, Heidelberg, Germany Hans-Richard Rackwitz, DKFZ, Heidelberg, Germany Hanspeter Saluz, HKI, Jena, Germany Birgit Simen, University of Chicago, USA Giulio Superti-Furga, EMBL, Heidelberg, Germany Martin Vingron, MPI, Berlin
Table of contents (general overview):

1. 1.1. 1.2. 1.3. 1.4. 1.5. 1.6. Working with DNA. . . . . . . . . . . 1 Precautions for handling DNA . . . 2 Commonly used formulas . . . . . . . 3 Isolating and purifying DNA . . . . . 6 Analyzing DNA. . . . . . . . . . . . . . . . 9 Cloning of DNA . . . . . . . . . . . . . . 22 Labeling of DNA and Oligonucleotides . . . . . . . . . . . . . 29 1.7. Amplification of DNA . . . . . . . . . 36 1.8. Quantitative Real-Time PCR . . . . 46 1.9. References . . . . . . . . . . . . . . . . . . 59 2. 2.1. 2.2. 2.3. 2.4. 2.5. 2.6. 2.7. Working with RNA . . . . . . . . . . 59 Precautions for handling RNA . . . 60 Commonly used formulas . . . . . . . 63 Isolating and purifying RNA . . . . . 65 Analyzing RNA . . . . . . . . . . . . . . . 68 RT-PCR . . . . . . . . . . . . . . . . . . . . . . 70 Labeling of RNA . . . . . . . . . . . . . . 79 References . . . . . . . . . . . . . . . . . . . 81 3. Working with Proteins . . . . . . . 81 3.1. Precautions for handling Proteins . . . . . . . . . . . . . 82 3.2. Conversion from Nucleic Acids to Proteins . . . . . . . . . . . . . . 88 3.3. Analyzing Proteins . . . . . . . . . . . . 92 3.4. Quantification of Proteins . . . . . . 98 3.5. Purifying Proteins . . . . . . . . . . . . 102 3.6. References . . . . . . . . . . . . . . . . . 112
Table of contents (general overview):

4. 4.1. 4.2. 4.3. 4.4 4.5. Working with Cells . . . . . . . . Precautions for handling Cells . Basic Information . . . . . . . . . . . . Manipulating Cells. . . . . . . . . . . Analyzing Cells. . . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . 112 113 . 117 123 131 144 6. Conversion Tables and Formulas . . . . . . . . . . . . . 163 6.1. Nucleotide ambiguity code . . . . . 164 6.2. Formulas to calculate melting temperatures . . . . . . . . . . . . . . . . 164 6.3. %GC content of different genomes . . . . . . . . . . . . . . . . . . . 165 6.4. Metric prefixes . . . . . . . . . . . . . . 165 6.5. Greek alphabet . . . . . . . . . . . . . . 166 6.6. Properties of radioisotopes. . . . . 166 6.7. Temperatures and Pressures. . . . . 167 6.8. Centrifugal forces . . . . . . . . . . . . 167 6.9. Periodical system of elements . . 168 6.10. Hazard Symbols . . . . . . . . . . . . . . 168 6.11. References . . . . . . . . . . . . . . . . . . 169 7. 7.1. 7.2. 7.3. 7.4. Addresses, Abbreviations and Index Selection of useful addresses Lab Steno . . . . . . . . . . . . . . . . Abbreviations . . . . . . . . . . . . . Alphabetical Index . . . . . . . . . . . . . . . . . 169 170 172 173 176
5. 5.1. 5.2. 5.3. 5.4.
Preparing Buffers and Media . . . . . . . . . . . . . . . Buffers . . . . . . . . . . . . . . . . . . . . Antibiotics . . . . . . . . . . . . . . . . . Media for Bacteria . . . . . . . . . . . References . . . . . . . . . . . . . . . . .
145 146 160 161 163
II
Table of contents (detailed overview):

1. Working with DNA . . . . . . . . . . . . . . . . . . . . 1
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3 .5 .6 .8 .8 9 .9 1.1. Precautions for handling DNA . . . . . . . . . . . . . . . . . 1.2. Commonly used formulas . . . . . . . . . . . . . . . . . . . . . Examples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.3. Isolating and purifying DNA . . . . . . . . . . . . . . . . . . Perform nucleic acid isolation rapidly and efficiently Sizes and weights of DNA from different organism . 1.4. Analyzing DNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Concentration and purity via OD measurement . . . . Fragment Sizes of DNA Molecular Weight Markers and recommended Types of Agarose . . . . . . . . . . . . . Size estimation of DNA fragments in Agarose MP gels . . . . . . . . . . . DNA fragments in Acrylamide gels . . . . . . . . . . . . Restriction Enzymes: General Information . . . . . . . . . . . . . . . . . . . . . . . . Buffer System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Star Activity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Reference Materials available . . . . . . . . . . . . . . . . . Inactivation and removal . . . . . . . . . . . . . . . . . . . . . Characteristics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cross index of recognition sequences . . . . . . . . . . Partial Digest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.5. Cloning of DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ligation with T4 DNA Ligase . . . . . . . . . . . . . . . . . . . . . Dephosphorylation with Shrimp Alkaline Phosphatase . Modifying sticky ends to blunt ends: 5protruding and 3recessed ends . . . . . . . . . . . . . . . . . Klenow for partial or complete filling of 3recessed ends . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mung Bean Nuclease for removing of 3 and 5 protruding ends . . . . . . . . . . . . . . . . . . . . . . . . Miscellaneous . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Commonly used bacterial strains . . . . . . . . . . . . . . . . . . 1.6. Labeling of DNA and Oligonucleotides . . . . . . . . . . . . General Considerations . . . . . . . . . . . . . . . . . . . . . . . . . Overview of different techniques . . . . . . . . . . . . . . . . . . Dig Labeling of Nucleic Acids . . . . . . . . . . . . . . . . . . . . Random Primed Labeling with Klenow . . . . . . . . . . . . . Nick Translation with DNA Polymerase I and DNAse I . 3End labeling with Terminal Transferase . . . . . . . . . . . . 5End labeling with Polynucleotide Kinase . . . . . . . . . . . . 22 . . .22 . . .23 . . .24 . . .25 . . . . . . . . . . . . . . . . . . . . . . .26 .27 .28 29 .29 30 31 .32 .33 34 .35
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1.7. Amplification of DNA . . . . . . . . . . . . . . . . . . . . . . Avoiding Contamination . . . . . . . . . . . . . . . . . . . . . Reaction Components: Template . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Primers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Oligonucleotides: Commonly used Formulas . Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Reaction Components: MgCl2 concentration . . . . . . . . . . . . . . . . . . . . dNTP concentration. . . . . . . . . . . . . . . . . . . . . Choice of Polymerase . . . . . . . . . . . . . . . . . . . Hot Start Techniques . . . . . . . . . . . . . . . . . . . . Other factors . . . . . . . . . . . . . . . . . . . . . . . . . . Cycling Profile for standard PCR . . . . . . . . . . . . . . Standard Pipetting Scheme . . . . . . . . . . . . . . . . . Standard PCR Temperature Profile . . . . . . . . . . . .
. . . . . . 36 . . . . . . .36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37 38 39 .40 40 41 41 .42 .42 .43 .44 .45
1.8. Quantitative Real-Time PCR . . . . . . . . . . . Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . Instrument-based Systems . . . . . . . . . . . . . Real-Time PCR Assay Formats . . . . . . . . . . Sequence-Independent Detection Assays . Sequence-specific Probe Binding Assays . Other Assay formats . . . . . . . . . . . . . . . . . . Principles of Quantification . . . . . . . . . . . . Melting Curve Analysis . . . . . . . . . . . . . . . . 1.9. References . . . . . . . . . . . . . . . . . . . . . . . . .
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46 46 .47 48 49 50 54 .57 .57 59
2.
Working with RNA . . . . . . . . . . . . . . . . . . . . 59

. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 63 64 65 .67
2.1. Precautions for handling RNA . . . . . . . . 2.2. Commonly used formulas . . . . . . . . . . . . Examples . . . . . . . . . . . . . . . . . . . . . . . . . . 2.3. Isolating and purifying RNA . . . . . . . . . . RNA content in various cells and tissues
III
2.4. Analyzing RNA . . . . . . . . . . . . . . . . . . . . . . . . Concentration via OD Measurement . . . . . . . Purity via OD Measurement . . . . . . . . . . . . . . Size estimation of RNA fragments . . . . . . . . 2.5. RT-PCR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Reaction Components: Template . . . . . . . . . . . . . . . . . . . . . . . . . Choice of reverse transcription primers Design of reverse transcription primers Template Design . . . . . . . . . . . . . . . . . . . Choice of enzymes . . . . . . . . . . . . . . . . . Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . Reaction Components: Choice of enzyme for Two Step RT-PCR Choice of enzyme for One Step RT-PCR 2.6. Labeling of RNA . . . . . . . . . . . . . . . . . . . . . . Overview of different techniques . . . . . . . . . Principle of In Vitro Transcription with DNA dependent RNA Polymerases . . . . SP6, T7 and T3 Polymerases . . . . . . . . . . . . . 2.7. References . . . . . . . . . . . . . . . . . . . . . . . . . . .
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68 .68 .68 .69 .70 .70 71 .72 .73 .75 .76 .77 .78 .79 .79
3.
Working with Protein. . . . . . . . . . . . . . . . . . 81

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3.1. Precautions for handling Proteins . . . . . . . . . . . . . . . Inhibition of protease activity . . . . . . . . . . . . . . . . . . . . Stabilization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.2. Conversions from Nucleic Acids to Proteins . . . . . . . Information transfer . . . . . . . . . . . . . . . . . . . . . . . . . . . The Genetic Code . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Characteristics of Amino Acids . . . . . . . . . . . . . . . . . . Codon Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.3. Analyzing Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . Separation ranges of proteins in denaturing SDS-PAGE . . . . . . . . . . . . . . . . . . . . . . . Sizes of commonly used markers in denaturing SDS-PAGE . . . . . . . . . . . . . . . . . . . . . . . Staining of proteins on denaturing SDS-PAGE gels . . Staining and detection of proteins on membranes . . . Buffer exchange via gel filtration . . . . . . . . . . . . . . . . . Properties of commonly used detergents: Definitions Characteristics of detergents . . . . . . . . . . . . . . . . . . . . Removal of detergents . . . . . . . . . . . . . . . . . . . . . . . . . Ammonium sulfate precipitation . . . . . . . . . . . . . . . . . Other precipitation techniques . . . . . . . . . . . . . . . . . .
. . . .92 . . . . . . . . . . . . . . . . . . . . . . . . . . . .92 .93 .93 94 94 95 96 96 .97
3.4. Quantification of Proteins . . . . . . . . . . . . . . . . . OD Measurement . . . . . . . . . . . . . . . . . . . . . . . . Assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Concentration limits of interfering reagents for assays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Compatibility of different buffer systems with protein quantification assays . . . . . . . . . . . 3.5. Purifying Proteins . . . . . . . . . . . . . . . . . . . . . . . . Characteristics of different expression systems Sources of antibodies . . . . . . . . . . . . . . . . . . . . . Expressing Proteins: Cell-free - Rapid Translation System . . . . . . . . . Choices of animals for immunization. . . . . . . . . Doses of immunogens for Rabbits . . . . . . . . . . Routes of injections for Rabbits . . . . . . . . . . . . . Purifying antibodies using Protein A, Protein G and Protein L . . . . . . . . . . . . . . . . . . . Immunoprecipitation . . . . . . . . . . . . . . . . . . . . . Ion Exchange Chromatography . . . . . . . . . . . . . Experimental setup . . . . . . . . . . . . . . . . . . . Tagging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3.6. References . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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4.
Working with Cells . . . . . . . . . . . . . . . . . . 112
4.1. Precautions for handling Cells . . . . . . . . . . . . . . . . . . . . . . . . 113 Tissue culture reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113 Growth areas and yields of cells in a culture vessels . . . . . . . 115 Mycoplasma Contamination . . . . . . . . . . . . . . . . . . . . . . . . . . . 116 Detection of Mycoplasma contamination . . . . . . . . . . . . . . . . .117 4.2. Basic Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .117 Typical Properties of Bacterial Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .117 of Plant Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118 of Animal Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118 Nucleic Acid and Protein content of a bacterial cell. . . . . . . . . . . . . . . 119 content in mammalian cells . . . . . . . . . . . . . . . . . . . . . . . 119 and Protein content in human blood . . . . . . . . . . . . . . . . 120 Cell Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121 Arresting Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122 4.3. Manipulating Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123 Transfection of mammalian cells . . . . . . . . . . . . . . . . . . . . . . . 123 DNA influences on transfection . . . . . . . . . . . . . . . . . . . . . . . . 124 Transfection protocol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 Time course of transfection . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
IV
Calcium phosphate-DNA coprecipitation . . . . . . . . . . . . . . . . 127 Liposomal and non-liposomal Transfection Reagents. . . . . . . 127 Electroporation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128 Voltage Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 Microinjection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130 Use of Selection Markers for Stable Cell Lines . . . . . . . . . . . . 130 4.4. Analyzing Cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131 Apoptosis/Necrosis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .131 Apoptosis Assay Methods . . . . . . . . . . . . . . . . . . . . . . . . . .134 Selection Guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .135 Cell Proliferation and Viability . . . . . . . . . . . . . . . . . . . . . . . .136 Proliferation Assay Methods: Selection Guide. . . . . . . . . . . .137 FACS (Fluorescence activated cell sorting). . . . . . . . . . . . . .138 Reporter Gene Assays Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .141 4.5. References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
5.
Preparing Buffers and Media . . . . . . . . . . 145

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5.1. Buffers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Definitions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Precautions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Buffering ranges of commonly used buffers (at 20C) . Recipes for stock solutions . . . . . . . . . . . . . . . . . . . . . . . . . . . . buffers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . buffers with desired pH . . . . . . . . . . . . . . . . . . . . . Electrophoresis of DNA . . . . . . . . . . . . . . . . . . . . . . . . . Electrophoresis of RNA . . . . . . . . . . . . . . . . . . . . . . . . . DEPC-treatment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Staining of Nucleic Acids . . . . . . . . . . . . . . . . . . . . . . . . Electrophoresis of Proteins . . . . . . . . . . . . . . . . . . . . . . Resolving gels for denaturing SDS PAGE . . . . . . . . . . 5% stacking gels for denaturing SDS-PAGE . . . . . . . . . Western Blotting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.2. Antibiotics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Selection of prokaryotic cells . . . . . . . . . . . . . . . . . . . . . . . . . . . eukaryotic cells . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5.3. Media for Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Recipes for 1 liter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . (for 40 plates of 90 mm, 25 ml per plate) . . . . 5.4. References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
6.
Conversion Tables and Formulars . . . . . . 163

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7.
7.1. 7.2. 7.3. 7.4.
Addresses and Index . . . . . . . . . . . . . . . . . 169

Selection of useful addresses . Lab Steno . . . . . . . . . . . . . . . . . Abbreviations . . . . . . . . . . . . . . Alphabetical Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170 172 173 176
6.1. Nucleotide ambiguity code . . . . . . . . . . . . . . . 6.2. Formulas to calculate melting temperatures . 6.3. %GC content of different genomes . . . . . . . . 6.4. Metric prefixes . . . . . . . . . . . . . . . . . . . . . . . . . 6.5. Greek alphabet. . . . . . . . . . . . . . . . . . . . . . . . . 6.6. Properties of radioisotopes . . . . . . . . . . . . . . . 6.7. Temperatures and Pressures. . . . . . . . . . . . . . 6.8. Centrifugal forces . . . . . . . . . . . . . . . . . . . . . . 6.9. Periodical system of elements . . . . . . . . . . . . 6.10. Hazard symbols and risk phrases . . . . . . . . . . 6.11. References . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Working with DNA

Chapter 1
1.1. 1.2. 1.3. 1.4. 1.5. 1.6. 1.7. 1.8. 1.9.
Precautions for handling DNA ........................................ 2 Commonly used formulas .................................................. 3 Isolating and purifying DNA ............................................. 6 Analyzing DNA ...................................................................... 9 Cloning of DNA ................................................................... 22 Labeling of DNA and Oligonucleotides ..................... 29 Amplification of DNA ........................................................ 36 Quantitative Real-Time PCR ........................................... 46 References ............................................................................ 59
1.1.
Precautions for handling DNA

For the isolation of genomic DNA from cells and tissues, use either fresh samples or samples that have been quickly frozen in liquid nitrogen and stored at 70C. This procedure minimizes degradation of the DNA by limiting the activity of endogenous nucleases. For best results, use fresh blood or blood stored for < 2 days at room temperature. Blood stored for 7 days at 2-8C or for < 1 month at 15 to 25C will result in a 10 to 15% reduction of yield of genomic DNA. Collect blood samples in tubes containing EDTA as anticoagulant, not heparin. Heparin can cause attenuation or inhibition of amplification during PCR. However, if heparin cannot be avoided, the High Pure PCR Template Preparation Kit* can be used to remove the heparin from the sample. Avoid vigorous pipetting. Pipetting genomic DNA through small tip openings causes shearing or nicking. Use tips with wide openings, specially designed for genomic DNA. Regular pipette tips pose no problem for plasmid DNA and other small DNA molecules.
Handling fresh and stored material before extraction of DNA
Pipetting DNA
* Product available from Roche Applied Science: Cat. No. 11 796 828 001
Storage of DNA
Store genomic DNA at 2-8C, storage at 15 to 25C can cause shearing of the DNA. Plasmid DNA and other small DNA molecules can be stored at 2-8C for short term storage in aliquots at 15 to 25C for long term storage. Keep plasmids for transformation purposes at 2-8C to avoid nicks. Store modified DNA at 2-8C. Always keep the DNA sample on ice when preparing an experiment. Avoid overdrying of genomic DNA after ethanol precipitation. Let the DNA air dry. Plasmid DNA and other small DNA molecules can be air or vacuum dried. Dissolve DNA in Tris buffer (e.g., 10 mM Tris, pH 7.0 pH 8.0). To help dissolve the DNA, carefully invert the tube several times after adding buffer and/or tap the tube gently on the side. Alternatively, let the DNA stand in buffer overnight at 2-8C. Do not vortex genomic DNA. Heat DNA for 10 min. at 65C to dissolve and inactivate DNases.
Manipulation of DNA Drying DNA
Dissolving DNA
Working with DNA
1.2.
Commonly used formulas

Average molecular weight (MW) of a deoxynucleotide: 330 Dalton (Da)* Average molecular weight (MW) of a DNA basepair: 660 Dalton (Da)*
MW of dsDNA = [number of basepairs] x [660 Da]
Molecular Weight of DNA, Calculation in Dalton*
e.g., MW of pBR322 dsDNA (4 363 basepairs)
= 4 363 x 660 Da = 2.9 x 10 6 Da = 2.9 x 103 kDa
MW of ssDNA = [number of bases] x [330 Da]
e.g., MW of M13mp18 (7 249 bases, ssDNA form)= 7 249 x 330 Da = 2.4 x 10 6 Da = 2.4 x 103 kDa
* 1 Da (Dalton) is a unit of mass almost equal to that of a hydrogen atom (precisely equal to 10000 on the atomic mass scale). Named after John Dalton (1766 1844) who developed the atomic theory of matter.
Calculation of pmol of 5 (or 3) ends
pmol of ends of a dsDNA molecule

= 2 x 10 6 x g (of dsDNA) MW (in Da) = 2 x 10 6 x g (of dsDNA) Nbp x 660 Da 2 x 10 6 x 1 = 30.3 100 x 660
e.g., pmol of 5or 3ends of 1 g of a 100 basepairs dsDNA fragment =
pmol of ends of a ssDNA molecule

= 1 x 10 6 x g (of ssDNA) MW (in Da) = 1 x 10 6 x g (of ssDNA) Nb x 330 Da 1 x 10 6 x 1 250 x 330 = 12.12
e.g., pmol of 5or 3ends of 1 g of a 250 bases ssDNA fragment =
pmol of ends generated by restriction endonuclease cleavage: circular DNA: 2 x (pmol of DNA) x (number of sites) linear DNA: [2 x (pmol of DNA) x (number of sites)] + [2 x (pmol of DNA)]
Nbp = number of basepairs (dsDNA) and Nb = number of bases (ssDNA)
Working with DNA
1.2.

pmol of dsDNA = g (of dsDNA) x 10 6 pg 1 pmol 1 g (of dsDNA) x 1515 x x = 1 g 660 pg Nbp Nbp 1 x 1 515 = 15.2 pmol 100
Conversion of g to pmol
e.g., 1 g of a 100 basepairs dsDNA fragment =
pmol of ssDNA = g (of ssDNA) x
1 g (of ssDNA) x 3 030 10 6 pg 1 pmol x x = 1 g 330 pg Nb Nb 1 x 3 030 = 3.03 pmol 1 000
e.g., 1 g of a 1 000 bases ssDNA fragment =
Conversion of pmol to g
g of dsDNA = pmol (of dsDNA) x
660 pg 1 g x x Nbp = 1 pmol 106 pg
= pmol (of dsDNA) x Nbp x 6.6 x 10-4 e.g., 1 pmol of a 100 basepairs dsDNA fragment = 1 x 100 x 6.6 x 10-4 = 0.066 g
g of ssDNA = pmol (of ssDNA) x
330 pg 1 g x x Nb = 1 pmol 10 6 pg
= pmol (of ssDNA) x Nb x 3.3 x 10-4 e.g., 1 pmol of a 250 bases ssDNA fragment = 1 x 250 x 3.3 x 10-4 = 0.0825 g
Nbp = number of basepairs (dsDNA) and Nb = number of bases (ssDNA)
Working with DNA
1.2.
Type

Examples
Size 100 bp 500 bp 1 000 bp Form Linear Linear Linear RE* Digest, 1 site RE* Digest, 2 sites 1.8 x 103 MW (in kDa) 66 330 660 pmol/g 15.2 3.03 1.52 1.52 1.52 0.57 0.57 0.57 0.57 2.9 x 103 0.35 0.35 0.35 0.35
g/pmol
pmol of 5 or 3 ends/g 30.3 6.06 3.03 6.06 9.12 1.14 2.28 3.42 0.7 1.4 2.1
dsDNA fragment dsDNA fragment dsDNA fragment
0.066 0.33 0.66 0.66 0.66 1.77 1.77 1.77 1.77 2.88 2.88 2.88 2.88
pUC18/19 dsDNA
2 686 bp
Circular RE* Digest, 1 site RE* Digest, 2 sites RE* Digest, 3 sites
pBR322 dsDNA
4 363 bp
Circular RE* Digest, 1 site RE* Digest, 2 sites RE* Digest, 3 sites
* RE: restriction enzyme
Notes
Working with DNA
1.3.
Type
Isolating and purifying DNA

Origin tissue, cultured cells, bacteria, yeast tissue, cultured cells, bacteria, yeast, mouse tail human blood mammalian/human blood Recommendation* High Pure PCR Template Preparation Kit DNA Isolation Kit for Cells and Tissues High Pure PCR Template Preparation Kit DNA Isolation Kit for Mammalian Blood High Pure Plasmid Isolation Kit Genopure Plasmid Maxi/Midi Kits High Pure Viral Nucleic Acid Kit High Pure 16 System Viral Nucleic Acid Kit High Pure PCR Product Purification Kit PCR mixture, restriction enzyme digests, labeling and modifying reactions, DIG labeled probes. High Pure 96 UF Cleanup Kit High Pure PCR Cleanup Micro Kit Mini Quick Spin DNA Columns Quick Spin Columns Agarose Gel DNA Extraction Kit agarose gel slices High Pure PCR Product Purification Kit High Pure PCR Cleanup Micro Kit
Use this chart to select a product according to the type and origin of DNA (see also reference 4).
Genomic
Plasmid Viral
propagated in E.coli serum, plasma, blood, other body fluids, cell culture supernatant serum, plasma, cell culture supernatant
DNA fragments
removal of unincorporated nucleotides from labeled DNA molecules
* The amount of DNA that can be isolated with the kits depends on variables like the amount of sample applied, concentration of DNA within the sample, buffers systems, etc. Please refer to the next pages for a detailed overview.
Use this chart to select a product according to the main application in which the DNA will be used (see reference 4).
Product PCR Restriction Enzyme Analysis Southern Blotting Labeling/ Modifying Reactions Cloning Sequencing In Vitro Transcription Trans fection Microarray spotting
DNA Isolation Kit for Cells and Tissues DNA Isolation Kit for Mammalian Blood High Pure Plasmid Isolation Kit High Pure Viral Nucleic Acid Kit High Pure 16 System Viral Nucleic Acid Kit High Pure PCR Template Preparation Kit High Pure 96 UF Cleanup Kit High Pure PCR Product Purification Kit High Pure PCR Cleanup Micro Kit Mini Quick Spin DNA Columns Quick Spin Columns Agarose Gel DNA Extraction Kit Genopure Plasmid Midi Kit Genopure Plasmid Maxi Kit
Working with DNA
1.3.
Product

Quantity of starting material Agarose slices: 100 200 mg Typical Yield Recovery:
0.1 10 kb: ~ 80% 10 kb 100 kb: ~ 60% Oligos > 20 bases: ~ 60%
Use this chart to select a product according to its characteristics (see also reference 4)
Agarose Gel DNA Extraction Kit
DNA Isolation Kit for Cells and Tissues
Tissue: up to 1 g Cultured cells: up to 5 x 107 cells Mouse tail: up to 400 mg Yeast: up to 3 x 10 10 cells Gram neg. bacteria: up to 10 11 cells Human whole blood: 10 ml Rat and mouse whole blood: 10 ml 100 bp to > 10 kb 20 to 300 . E. coli XL1 Blue, pUC19 2 ml E. coli DH5, pUC19 2 ml 200 600 l of serum, plasma, blood, cell culture supernatant 200 600 l of serum, plasma, blood, cell culture supernatant
depending on tissue type 700 3 000 g up to 800 g up to 300 g 1 500 2 700 g 350 g 570 g 25 l ( 150 bp 40%; 1500 bp 90%; 4500 bp 90%; 8000 bp 80%) 12 g 3.5 g product detectable by PCR product detectable by PCR
DNA Isolation Kit for Mammalian Blood High Pure 96 UF Cleanup Kit
High Pure Plasmid Isolation Kit High Pure Viral Nucleic Acid Kit High Pure 16 System Viral Nucleic Acid Kit
Use this chart to select a product according to its characteristics (see also reference 4)
Product High Pure PCR Template Preparation Kit Quantity of starting material Blood: up to 300 l Cultured cells: up to 10 8 cells Mouse tail: 25 50 mg Yeast: 10 8 cells Bacteria: 10 9 cells 100 l of a modifying, labeling or restriction enzyme digestion reaction up to 100 l reaction mix up to 100 mg agarose gel slice 20 75 l labeling mixture Typical Yield 3 9 g 15 20 g 5 10 g 10 13 g 1 3 g Recovery: > 80% of 5 25 g DNA (fragments > 100 bp) Recovery: > 80% of 5 25 g DNA (fragments > 100 bp) Recovery: > 90% Exclusion limit: 20 bp 0.2 1 g/ml culture (low copy plasmid) 3 5 g/ml culture (high copy plasmid) 0.2 1 g/ml culture (low copy plasmid) 3 5 g/ml culture (high copy plasmid)
High Pure PCR Product Purification Kit High Pure PCR Cleanup Micro Kit Mini Quick Spin DNA Columns
Genopure Plasmid Midi Kit
10 100 ml bacterial culture (low copy plasmid) 5 30 ml bacterial culture (high copy plasmid) 100 500 ml bacterial culture (low copy plasmid) 30 150 ml bacterial culture (high copy plasmid)
Genopure Plasmid Maxi Kit
Note: For more information on nucleic acid isolation and purification please visit http://www.roche-applied-science.com/napure
Working with DNA
1.3.

Perform nucleic acid isolation rapidly and efficiently
The MagNA Pure LC Instrument allows fully automated nucleic acid isolation and PCR setup. True walkaway precision is achieved with the elimination of hands-on steps such as pipetting, filtration, and centrifugation. With the MagNA Pure LC Instrumentss proven magnetic bead technology, high quality genomic DNA, total RNA, or mRNA is obtained. The MagNA Pure LC Instrument processes up to 32 samples in less than one hour and isolates pure nucleic acids from a variety of sample types, including:

Whole blood Cultured cells
White blood cells Tissues
Expand the MagNA Pure LC Instruments flexibility and versatility with the use of various reagent kits, accessories, and software protocols:
DNA Isolation Kits Total Nucleic Acid Isolation Kits
- for blood/cultured cells, tissue, and bacteria/fungi - for blood, plasma, and serum; also available for large volumes RNA Isolation Kits - for whole blood, blood cells, cultured cells, and paraffin-embedded tissue mRNA Isolation Kits - for whole blood, blood cells, and tissue
Increase your labs efficiency by combining the MagNA Pure LC Instrument with the LightCycler Carousel Centrifuge and the LightCycler Instrument.
Note: For more information on MagNA Pure LC please visit http://www.magnapure.com
Sizes and weights of DNA from different organism

Organism pBR322, E. coli plasmid SV 40, Simian virus X174, E.coli bacteriophage Adenovirus 2, human virus Lambda, E.coli bacteriophage E.coli, bacterium Saccharomyces cerevisiae, yeast Dictyostelium discoideum, mold Caenorhabditis elegans, worm Drosophila melanogaster, fruitfly Mus musculus, mouse Xenopus leavis, frog Homo Sapiens, human Zea mays, maize Nicotiana tabacum, tabacum plant Size (bp) 4 363 5 243 5 386 35 937 48 502 4.7 x 10 1.5 x
6
Molecular Weight (in kDa) 2.9 x 103 3.5 x 103 3.5 x 103 23.7 x 103 32.0 x 103 3.1 x 10 6 9.9 x 10 6 3.6 x 107 5.3 x 107 9.2 x 107 1.8 x 10 9 2.0 x 10 9 2.2 x 10 9 2.6 x 10
9
Number of Chromosomes
107
32 (diploid) 7 (haploid) 11/12 (diploid) 8 (diploid) 40 (diploid) 36 (diploid) 46 (diploid) 20 (diploid) 48 (diploid)
5.4 x 107 8.0 x 107 1.4 x 10 8 2.7 x 10

9
3.1 x 10 9 3.3 x 10 9 3.9 x 10

9
4.8 x 10 9
3.2 x 10 9
Working with DNA
1.4.
Analyzing DNA
Concentration and purity via OD measurement
Concentration of DNA Notes
1 A260 Unit of dsDNA = 50 g/ml H2O 1 A260 Unit of ssDNA = 33 g/ml H2O OD value should range between 0.1 and 1.0 to ensure an optimal measurement. The above mentioned values are based on extinction coefficients of nucleic acids in H2O, please note that these coefficients and hence the above mentioned values differ in other buffers and/or solutions. Example of calculation: volume of dsDNA sample: 100 l dilution: 25 l of this sample + 475 l H2O (1+19 dilution) A260 of this dilution: 0.44 concentration of dsDNA in sample: 0.44 x 50 g/ml x 20 (=dilution factor) = 440 g/ml amount of dsDNA in sample: 440 g/ml x 0.1 ml (= sample volume) = 44 g Pure DNA: A260/A280 1.8
Purity of DNA
Notes
An A260/A280 < 1.8 indicates that the preparation is contaminated with proteins and aromatic substances (e.g., phenol). An A260/A280 > 2 indicates a possible contamination with RNA. The OD gives no information about the size of the DNA.
Working with DNA
Fragment Sizes of DNA Molecular Weight Markers

II
10 528 552 001
0.12-23.1 kbp DNA Hind III
III
0.12-21.2 kbp DNA Eco RI + Hind III
IV
0.07-19.3 kbp DNA pSPTBM 20 DNA Sty I + Sau I
V
8-587 bp pBR 332 DNA Hae III
VI
0.15-2.1 kbp pBR 328 DNA Bgl I + pBR 328 DNA HinI I
VII
11 209 264 001 11 336 045 001
0.08-8.57 kbp SPP I DNA Eco RI
VIII
0.019-1.11 kbp pUC BM 21 Hpa II + pUC BM 21 DNA Dra I + Hind III
10 236 250 001
11 418 009 001
10 821 705 001
11 062 590 001
base pairs 70,000
23130 10,000 9416
21226
19329
7743 6557 4361 5148, 4973 4268 3530 3140 2690 2322 2027 2027 1904 1584 1375 1150 1,000 -947 831 697 564 564 587 540 504 458, 434 267 234 213 -192, 184 124, 123 104 89, 80 64, 57, 51, 21, 18, 11, 8 653 517 453 -394 298 234, 220 154 925 1230 1033 2322 2176 1882 1766 -1489 5526 4254
8576 7427 6106 4899 3639 2799
1953 1882 1515 1482 1164 992 900 710 (718*) 492 359 692 501, 489 404 320 242 -190 147 124 110 67 37, 34, 26, 19 1114
421
125 100 50
125 74
IX
0.072-1.35 kbp X 174 Hae III
X
0.075-12.21 kbp 1018 bp DNA fragment multimers and pBR 322 DNA fragments
XIII
50 bp ladder
XIV
11 721 615 001
100 bp ladder
XV
Expand DNA molecular weight marker
XVI
250 bp ladder
XVII
11 855 646 001
500 bp ladder
11 449 460 001
11 498 037 001
11 721 925 001
11 721 933 001
11 855 638 001
12216 11198 10180 9162 8144 7126 6108 5090 -4072 3054
48502 38412 32745 29027 26718 24918 22010 20323, 19944 18780 16710 15262, 15258 14183 13282, 12379 11848, 11205 10086, 9688 8113 7601
3574 2642 2642 2392 3000 2750 2500 2250 2000 1750 1500 1400 1300 1200 1100 1000 900 800 700 600 500 400 300 250 200 1500 1250 1000 750
5000 4500 4000 3500 3000 2500
2036 1636 1353 1078 872 750 700 650 600 -550 500 450 400 350 300 250 200 150 100 50 018
2000
1500
1000
603 517, 506 396 344 298 220, 201 154, 134, 75
500
500
310 281, 271 234 -194 118 72
100
Agarose MS 0.05 Kbp 1.5 Kbp Agarose LE 0.2 Kbp 15 Kbp Agarose MP 0.1 Kbp 30 Kbp
Working with DNA
10
1.4.
Analyzing DNA
Size estimation of DNA fragments in Agarose MP* gels
% Agarose MP 0.4% 30 kbp 25 kbp 15 kbp 10 kbp 0.8% 1% 1.25% 1.5% 2%
Range of separation of linear ds fragment sizes
7.5 kbp 5 kbp 2.5 kbp 1 kbp 500 bp 250 bp 100 bp 0 bp
approximate migration of Xylene Cyanol
approximate migration of Bromophenol Blue
* Agarose Multi Purpose (Cat. No. 11 388 983 001) available from Roche Applied Science is a high gel strength agarose (> 1800 g/cm2; 1%) permitting the use of very low and very high concentrations, resulting in a broad range of DNA molecules that can be separated in the same type of agarose. Please refer to chapter 5 Preparing Buffers and Media for recipes to prepare all necessary buffers.
Size estimation of DNA fragments in Acrylamide gels

% of Acrylamide/Bisacrylamide (29:1) 3.5% 1000 bp 750 bp 500 bp Efficient range of separation of linear ds fragment sizes 250 bp 100 bp 75 bp 50 bp 25 bp 5 bp 0 bp approximate migration of Xylene Cyanol approximate migration of Bromophenol Blue 5% 8% 12% 15% 20%
Please refer to chapter 5 Preparing Buffers and Media for recipes to prepare all necessary buffers.
Working with DNA
11
1.4.
Analyzing DNA
Restriction Enzymes: General Information
Unit definition
One unit of a restriction endonuclease is the amount of enzyme required to completely digest 1 g substrate DNA in 60 min. at the appropriate assay conditions stated for each restriction enzyme. The type of the substrate DNA, the correct reaction temperature and the specific activity of each enzyme are stated in the packinserts that come together with the products. (Compare to page 14 table section Sub) All restriction enzymes supplied by Roche Applied Science contain expiry dates on the label. 100% activity of the enzyme is guaranteed until that date. Restriction enzymes are, like all proteins, susceptible to denaturation and can loose their specific activity when exposed to higher temperatures. Therefore, the enzymes are supplied as a glycerol solution and should be stored at 15 to 25C in a non-defrosting freezer. During usage, it is recommended to keep the enzyme on ice or in specially developed benchtop coolers.
Stability
Storage
Note: For detailed information concerning restriction enzymes please visit: www.restriction-enzymes.com
Restriction Enzymes: Buffer System
SuRE/Cut Buffer System* buffers supplied as 10 x concentrated solutions:

Final Concentration in mM Buffer components Tris Acetate Tris HCl Magnesium Acetate MgCl2 Potassium Acetate NaCl 1,4-Dithioerythritol (DTE) 1,4-Dithiothreitol (DTT) 2-Mercaptoethanol pH at 37C 7.9 0.5 1 8.0 7.5 7.5 7.5 66 100 1 50 1 100 1 10 5 10 10 10 A 33 10 10 10 50 B L M H
Special incubation buffers** buffers supplied as 2 x concentrated solutions:

Final Concentration in mM Buffer components Tris HCl NaCl MgCl2 2-Mercaptoethanol Bovine Serum Albumin (BSA) 1,4-Dithiothreitol (DTT) pH 8.0 (45C) 8.8 (50C) 8.2 (55C) Mae I 20 250 6 7 Mae II 50 220 6 7 100 g/ml 0,5 7.6 (37C) Mae III 20 275 6 7 Nde II 50 75 5
* Buffer system available from Roche Applied Science **Products available from Roche Applied Science
Working with DNA
12
1.4.
Analyzing DNA
Restriction Enzymes: Star Activity
Definition
The ability of restriction enzymes to cleave under non-optimal conditions DNA sequences that are similar but not identical to the recognition site of the enzyme. The following enzymes can exhibit star activity under certain non-optimized conditions: BamH I, BssH II, Dde I, EcoR I, EcoR V, Hind III, Hinf I, Kpn I, Mam I, Pvu II, Sal I, Sau3A I, SgrA I, Taq I However, reports (see ref. 12) suggest that star activity may be a general property of all restriction enzymes. High glycerol concentration (> 5% v/v). Large excess of enzyme. Non-optimal ionic strength, pH and divalent cations of buffer system. Presence of organic solvents. Use the optimal buffer for each enzyme as recommended by its suppliers. Use the optimal amount of enzyme as recommended by its suppliers. Make sure that the DNA preparation is free of organic solvents that may have been used during isolation and/or purification of the DNA.
Enzymes affected
Factors causing star activity
Avoiding star activity
Restriction Enzymes: Reference Materials available
Learn more about our solutions for mapping & cloning by visiting our special interest site at:
www.restriction-enzymes.com
Search for the needed restriction enzyme with the easy-to-use online tool Benchmate RE Finder at:
www.roche-applied-science.com/benchmate The Restriction Enzymes FAQS and Ordering Guide supplying
The comprehensive Restriction Enzyme Poster well known as the information source for commercially available restriction enzymes and their recognition sequences.
technical information, including troubleshooting.
The Tools for Mapping and Cloning brochure supplying so-
lutions to support you in your daily research.
available from your local Roche Applied Science representative
Working with DNA
13
1.4.
Analyzing DNA
Restriction Enzymes: Inactivation and removal
The following procedures can be applied to inactivate restriction enzymes:

Inactivation
By heat treatment: Certain enzymes can be inactivated by heating. Please refer to the product characteristics tables on the next pages for enzyme specific information. By EDTA treatment: Alternatively, the enzyme can be inactivated by adding 0.5 M EDTA (pH 8.0) to a final concentration of 10 mM. By phenol/chloroform extraction: Extract the sample with phenol/chloroform and once with chloroform, precipitate the DNA with ethanol or iso-propanol. By silica absorption: Alternatively, the tedious and cumbersome phenol/chloroform extraction procedure can be omitted by using the High Pure PCR Product Purification Kit (Cat. No. 11 732 668 001) or High Pure PCR Cleanup Micro Kit (Cat. No. 04 983 955 001) available from Roche Applied Science.
Removal
Restriction Enzymes: Characteristics
Abbreviations and icons used in the tables:

A B L M H HI Percentage activity of enzyme in SuRE/Cut buffer A (100% in bold printed buffer) Percentage activity of enzyme in SuRE/Cut buffer B (100% in bold printed buffer) Percentage activity of enzyme in SuRE/Cut buffer L (100% in bold printed buffer) Percentage activity of enzyme in SuRE/Cut buffer M (100% in bold printed buffer) Percentage activity of enzyme in SuRE/Cut buffer H (100% in bold printed buffer) Incubation temperature of enzyme, temperatures in bold differ from the classical 37C Heat inactivation of enzyme: Y: Indicates that the enzyme can be inactivated by heat (15 min at 65C unless otherwise stated) N: Indicates that the enzyme cannot be inactivated by heat (see previous page for alternative procedures) Indicates sensitivity of enzyme for methylation dcm+ : indicates that the enzyme is blocked by dcm methylation dam+ : indicates that the enzyme is blocked by dam methylation CG+ : indicates that the enzyme is blocked by eukaryotic methylation No indication: the enzyme is not sensitive to any form of methylation Function tested for Pulse Field Gradient Electrophoreses : the enzyme is function tested by Roche Applied Science for PFGE experiments No indication: the enzyme is not function tested Percentage of enzyme activity in a standard PCR Mix (= 10 mM Tris HCl, pH 8.3 at 20C, 50 mM KCl, 1.5 mM MgCl2 , -substrate DNA, 200 M dNTPs and 2.5 U Taq DNA Polymerase in a final volume of 100 l) Test substrate: = phage Lambda; P = pBR332, A = Adeno 2, M = MWM VII / number of cleavage sites
MS
PFGE
PCR Sub
Enzymes available from Roche Applied Science in dual concentrations are indicated in bold.
Working with DNA
14
1.4.
Analyzing DNA
Restriction Enzymes: Characteristics (for abbreviations, see page 14)
Sequence A 100 100 5075 1025 5075 100 100 100 5075 5075 75100 1025 100 100 5075 100 75100 75100 B 010 010 100 100 75100 5075 2550 1025 100 100 100 1025 100 5075 75100 100 100 100 L 010 1025 010 1025 5075 2550 75100 5075 2550 1025 010 100 1025 75100 1025 75100 5075 75100 M 1025 010 75100 5075 75100 2550 100 5075 75100 5075 2550 2550 5075 100 5075 100 5075 75100 H 010 010 5075 2550 100 010 1025 010 75100 010 5075 010 1025 1025 100 2550 2550 2550 37 37 50 50 37 37 37 30 37 37 37 37 37 37 37 37 37 37 HI Y N Y
a
MS CG+ CG+
PFGE
PCR 25% < 5%
Sub / 10 P/2 / 58 / 40
Aat II Acc I Acs I Acy I Afl III Alu I Alw44 I Apa I Asp I Asp700 Asp718 I AspE I Ava I Ava II Avi II BamH I Ban II BbrP I
GACGT C GT (A,C)(T,G)AC (A,G) AATT(T,C) G(A,G) CG(C,T)C A C(A,G) (T,C)GT AG CT G TGCAC GGGCC C GACN NNGTC GAANN NNTTC G GTACC GACNNN NNGTC C (T,C)CG(A,G)G G G(A,T)CC TGC GCA G GATCC G(A,G)GC(T,C) C CAC GTG
N N Y N Y N N N Y Y Y N N Y N 100% CG
+
20%
/ 20 P/3
100% / 143 dcm , CG

+ +
100% 10%
/1 /2 / 24 /2 /9 /8 / 35 / 15 /5 /7 /3
dcm+
100% 20% < 5% 30% 100%
dcm+, CG+
Sequence Bcl I Bfr I Bgl I Bgl II Bln I BpuA I BseA I BsiW I BsiY I Bsm I BspLU11 I BssH II Bst1107 I BstE II BstX I Cel II Cfo I T GATCA C TTAAG GCC(N)4 NGGC A GATCT C CTAGG GAAGAC(N) 2/6 T CCGGA C GTACG CCNNNNN NNGG GAATGCN N A CATGT G CGCGC GTA TAC G GTNACC CCA(N)5 NTGG GC TNAGC GCG C
A 100 2550 2550 100 2550 1025 75100 2550 100 010 100 100 2550 75100 1025 2550 75100
B 100 2550 5075 100 5075 100 100 100 100 5075 100 100 5075 100 100 5075 5075
L 2550 75100 1025 2550 010 2550 010 1025 5075 010 2550 75100 010 2550 010 2550 100
M 100 100 2550 100 2550 2550 5075 75100 100 2550 5075 100 2550 5075 1025 2550 5075
H 100 2550 100 100 100 5075 2550 100 2550 100 100 75100 100 5075 100 100 2550 50 37 37 37 37 37 55 55 55 65 48 50 37 60 45 37 37
HI N Y Y N N N N Ya N N N N N N N N N
MS dam+
PFGE
PCR 100% 30%
Sub /8 /3 / 29 /6 /2 / 24 / 24
CG+
M/1 / 176 / 46 /2
CG+ CG+
100% 100%
/6 /3 / 13 / 13 /6
100% / 215
a Inactivation
by heating to 75C for 1 hour
Working with DNA
15
1.4.
Analyzing DNA
Restriction Enzymes: Characteristics (continued) (for abbreviations, see page 14)
Sequence A 100 5075 100 100 100 5075 100 2550 2550 100 5075 2550 100 100 5075 100 5075 100 B 100 75100 75100 75100 5075 75100 2550 100 5075 100 75100 100 5075 5075 5075 100 100 100 L 75100 2550 5075 100 100 5075 75100 2550 010 2550 025 010 75100 2550 75100 2550 2550 5075 M 100 2550 75100 100 5075 75100 5075 2550 2550 5075 5075 2550 100 5075 100 100 100 75100 H 100 100 75100 5075 010 100 1025 5075 100 100 100 5075 2550 1025 2550 5075 5075 100 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 HI N N N Y Y N Y N Y Y Y N Y N N Y Y N CG+ 100% 10% 50% dcm+ 10% CG+ 50% CG+, dcm+ dcm+ 50% MS CG+, dam+ PFGE PCR 100% 40% 100% 100% Sub / 15 / 104 P / 22 / 13 P /4 / 10 / 39 /2 /2 /5 A / 136 / 21 P / 12 / 48 100% / 149 / 35 /6 / 148
Cla I Dde I Dpn I Dra I Dra II Dra III Eae I EclX I Eco47 III EcoR I EcoR II EcoR V Fok I Hae II Hae III Hind II Hind III Hinf I
AT CGAT C TNAG GA TC TTT AAA (A,G)G GNCC(T,C) CACNNN GTG (T,C) GGCC(A,G) C GGCCG AGC GCT G AATTC CC(A,T)GG GAT ATC GGATG(N)9/13 (A,G)GCGC (T,C) GG CC GT(T,C) (A,G)AC A AGCTT G ANTC
Sequence Hpa I Hpa II Ita I Kpn I* Ksp I Ksp632 I Mae I** Mae II** Mae III** Mam I Mlu I MluN I Mro I Msp I Mun I Mva I Mvn I GTT AAC C CGG GC NGC GGTAC C CCGC GG CTCTTC(N)1/4 C TAG A CGT GTNAC GATNN NNATC A CGCGT TGG CCA T CCGGA C CGG C AATTG CC (A,T)GG CG CG
A 100 5075 010 75100 010 100 2550 010 010 75100 1025 100 100 100 5075 100 5075
B 2550 2550 2550 1025 010 010 2550 2550 1025 75100 2550 010 010 100 010 5075 010
L 2550 100 010 100 100 2550 010 010 010 75100 010 1025 5075 100 100 2550 5075
M 5075 5075 010 2550 010 2550 010 2550 010 75100 1025 1025 5075 100 100 2550 100
H 2550 1025 100 010 010 010 1025 75100 1025 100 100 010 010 5075 1025 100 1025 37 37 37 37 37 37 45 50 55 37 37 37 37 37 37 37 37
HI N Y Y N N N N N N Y N Y N Y N N N
MS CG+ CG+
PFGE
PCR 100% 40% 50%
Sub / 14 / 328 / 380 /2 / 34 /4 / 14***
CG+ dam+ CG+ 20% < 5%
/ 143 / 156 / 22 /7 / 18 / 24 40% / 328 /8 / 71 30% / 157
* Requires addition of bovine serum albumin, 100 g/ml ** Mae I, Mae II, Mae III and Nde II require special incubation buffers which are supplied with each enzyme *** referred to cl 857Sam7
Working with DNA
16
1.4.
Analyzing DNA
Sequence A 100 100 5075 2550 1025 100 1025 1025 5075 2550 100 2550 5075 2550 75100 100 75100 100 B 010 75100 5075 75100 1025 2550 5075 100 100 5075 100 2550 75100 2550 100 5075 1025 010 L 100 75100 5075 1025 010 100 010 010 1025 75100 1025 1025 2550 2550 2550 100 100 100 M 010 5075 5075 5075 010 100 2550 1025 5075 100 5075 2550 5075 100 5075 5075 75100 5075 H 010 010 100 100 1025 1025 100 75100 100 010 5075 100 100 2550 2550 010 010 010 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 37 HI Y Y Y Y N Y Y Y Y N Y N N N Y Y N Y CG+ CG+ 100% CG+ CG+ 90% < 5% 100% dam+, CG+ 75% 100% dam+ CG+ 100% MS CG+ CG+ 50% PFGE PCR Sub P/ 4 A / 20 / 4 /7 / 116 /1 A/7 /5 / 14 / 32 / 13 / 28 /3 / 15 /8 100% / 113 /5 /2
Nae I Nar I Nco I Nde I Nde II** Nhe I Not I Nru I Nsi I Nsp I PinA I Pst I Pvu I Pvu II Rca I Rsa I Rsr II Sac I
GCC GGC GG CGCC C CATGG CA TATG GATC G CTAGC GC GGCCGC TCG CGA ATGCA T (A,G)CATG (T,C) A CCGGT CTGCA G CGAT CG CAG CTG T CATGA GT AC CG G(A,T)CCG GAGCT C
Sequence Sal I Sau3A I Sau96 I Sca I ScrF I SexA I Sfi I Sfu I SgrA I Sma I SnaB I Spe I Sph I Ssp I Stu I Sty I G TCGAC GATC G GNCC AGT ACT CC NGG A CC(A,T)GGT GGCC(N)4 NGGCC TT CGAA C(A,G) CCGG(T,C)G CCC GGG TAC GTA A CTAGT GCATG C AAT ATT AGG CCT C C(A,T)(A,T)GG
A 010 100 100 010 1025 100 2550 2550 100 100 75100 75100 5075 75100 100 5075
B 2550 2550 5075 100 100 100 2550 5075 010 010 2550 75100 75100 75100 100 100
L 010 2550 2550 010 1025 5075 75100 1025 100 010 100 75100 2550 1025 100 1025
M 1025 75100 2550 75100 1025 5075 100 2550 1025 010 100 100 100 75100 75100 75100
H 100 010 2550 100 5075 2550 2550 100 010 010 1025 100 75100 100 5075 100 37 37 37 37 37 37 50 37 37 25 37 37 37 37 37 37
HI Y N N N Y Y N N N Y N Y Y Y Y Y
MS CG+ CG+ dcm+, CG +
PFGE
PCR
Sub /2
100% / 116 / 74 < 5% /5 / 185 /5 10% A/ 3 /7 /6
dcm+ dcm+
CG+ CG
+
100% 50%
/3 /1 A/ 3 /6 / 20 /6 / 10
< 5% dcm+
30% < 5%
Inactivation by heating to 75C for 15 min ** Mae I, Mae II, Mae III and Nde II require special incubation buffers which are supplied with each enzyme
Working with DNA
17
1.4.
Analyzing DNA
Sequence A 010 5075 100 2550 100 2550 5075 5075 B 1025 100 2550 100 75100 75100 2550 010 L 010 2550 100 010 75100 1025 100 100 M 010 5075 100 2550 75100 2550 75100 75100 H 100 5075 2550 010 100 100 010 010 25 65 65 37 37 37 37 37 HI N N N Y N N N N dam+ CG+ 60% < 5% dam+ MS PFGE PCR Sub A/ 1 100% / 121 / 195 / 14 /1 /1 P/ 8 /3
Swa I Taq I Tru9 I Van91 I Xba I Xho I Xho II XmaC I
ATTT AAAT T CGA T TAA CCA(N)4 NTGG T CTAGA C TCGAG (A,G) GATC(T,C) C CCGGG
Please note: For detailed information concerning restriction enzymes, please consult our Benchmate tool at http://www.roche-applied-science.com/benchmate
Working with DNA
18
1.4.
Analyzing DNA
Restriction Enzymes: Cross index of recognition sequences
Palindromic tetra nucleotide sequences:

AATT
ACGT
AGCT
ATAT
CATG
CCGG
CGCG
CTAG
GATC Dpn II Nde II Sau3A I
GCGC
GGCC
GTAC
TATA
TCGA
TGCA
TTAA
Tsp509 I
Mae II
Msp I Hpa II Alu I CviJ I Mvn I FnuD II
Mae I
HinP1 I
Csp6 I
Taq I
Tru9 I
Dpn I
Hae III CviJ I
Rsa I
CviR I
Cfo I
Tai I
Nla III
Cha I
Sequences are written in 5 to 3direction, arrows indicate the point of cleavage Enzymes in blue recognize only 1 sequence, enzymes in black recognize multiple sequences
Palindromic penta nucleotide sequences:

AA TT

AC GT AG CT
AT AT
CA TG CC GG CG CG CT AG GA TC GC GC GG CC GT AC BssK I Dde I ScrF I Hinf I Ita I Fmu I Sau96 I Mae III
TA TA
TC GA TG CA
TT AA
N N N N N N
Tsp4C I
A T A T
A
EcoR II Tfi I Mva I Tse I Ava II
A T A T A T

G C G C
C
Tsp45 I
Nci I
G C G C G C
Working with DNA
19
1.4.
Analyzing DNA
Restriction Enzymes: Cross index of recognition sequences (continued)
Palindromic hexa nucleotide sequences:

AATT
G C
ACGT
AGCT
ATAT
CATG
CCGG NgoM IV Cfr10 I
CGCG BssH II
CTAG Nhe I
GATC BamH I Xho II
GCGC Kas I Ban I Nar I Acy I
GGCC Bsp120 I
GTAC Asp718 Ban I
TATA
TCGA Sal I
TGCA Alw44 I
TTAA
EcoR I Acs I Acy I
Acc I
Acc I Hpa I Hind II
Ecl136 II
EcoR V
Nae I
Sfo I
Bst1107 I
Hinc II
Aat II
Sac I Ban II AspH I Bsp1286 I
Sph I Nsp I BseA I Mro I BsaW I
Bbe I Hae II
Apa I Ban II Bsp1286 I Eae I
Kpn I
Bsp1286 I Asp HI
Rca I
Xba I
Bcl I
SspB I
Sfu I SnaB I BsaA I
Nru I
Avi II
MluN I
Dra I
Palindromic hexa nucleotide sequences:

AATT
A T
ACGT
AGCT Hind III
ATAT
CATG
CCGG
CGCG Mlu I Afl III
CTAG Spe I
GATC Bgl II Xho II
GCGC
GGCC
GTAC
TATA
TCGA
TGCA
TTAA
Acs I
PinA I BspLU11 I Cfr10 I Afl III BsaW I
Psp1406 I
Cla I BspD I Ssp I Eco47 III Stu I Sca I
Asn I
Nsp I Nco I Sty I Dsa I Nde I BbrP I BsaA I Pvu II MspA1 I XmaC I Ava I BsoB I
Hae II Xho I Ava I BsoB I Sml I
Nsi I
Mun I
Dsa I
Bln I Sty I
EclX I Eae I
BsiW I
Sfc I
Sfc I
Bfr I Sml I
Sma I
MspA1 I Pvu I BsiE I
Ksp I
BsiE I
Pst I
Working with DNA
20
1.4.
Analyzing DNA
Partial Digest
Please keep in mind that this method could be of limited usefulness because the number of possible partial digestion products quickly becomes unmanageable as the number of restriction sites increases. For example, in a linear DNA module: number of restriction sites number of possible partialdigestion products 1 0 2 2 3 5 4 5 6
9 14 20
In general, the number of partial-digestion products (F) of a linear DNA molecule that contains N restriction sites is given by the formula FN+1 = N2 + 3N 2
Principle
Ethidium bromide intercalates into dsDNA thereby reducing enzymatic activity of most restriction endonucleases and resulting in a partial digestion of DNA. Pipetting scheme for Restriction digest Total reaction volume 50.0 l plasmid DNA 2.0-5.0 g Restriction enzyme 5 Units Distribute reaction mixture in 5 Eppendorf tubes containing ethidium bromide to final concentrations of 0, 0.02, 0.01, 0.002, 0.005 mg per ml Incubate at 37 C for 20 min Load on gel
Working with DNA
21
1.5.
Cloning of DNA
Ligation with T4 DNA Ligase*
Properties
Catalyzes the formation of phosphodiester bonds between adjacent 3-OH and 5-P ends in dsDNA. Closes single-stranded nicks in dsDNA. Needs ATP as co-factor. 660 mM Tris, 50 mM MgCl2, 50 mM DTT, 10 mM ATP, pH 7.5 at 20C. Buffer is stable at 15 to 25C, store in aliquots. Note: ATP is not stable and decreased concentrations of ATP negatively influence the ligation efficiency: aliquot Ligation buffer, store at 20C and add to ligation mix before use. The new Rapid DNA Dephos & Ligation Kit (Cat. No. 04 898 117 001) available from Roche Applied Science enables fast and efficient dephosphorylation and ligation of sticky- or blunt-end DNA fragments. The convenient kit enables ligation of DNA in 5 minutes and dephosphorylation in 10 minutes. Note: this kit contains PEG and cannot be used without further purification of the ligation mix for transformation of bacteria via electroporation. Sticky ends: when vector DNA and insert DNA are ~ similar in length: a molar ratio of 1: 3 (vector versus insert DNA) is recommended.
Ligation buffer, 10 x
Tip
Molar ratio of vector and fragment DNA
when vector DNA and insert DNA are not similar in length: a molar ratio of 1:1 or 1:2 (vector versus insert DNA) is recommended. Blunt ends: a molar ratio of vector DNA to insert DNA of 1: 5 is recommended.
Application and typical results
Standard Assay: Ligation of DNA fragments:

Components Template DNA 10 x Ligation buffer T4 DNA Ligase H2 O Incubation Sticky ends up to 1 g digested DNA 3 l 1 5 units Add up to 30 l 4 to 16C, overnight Blunt ends up to 1 g digested DNA 3 l 1 5 units Add up to 30 l 16 to 25C, overnight
Sticky ends: > 95% of the DNA is ligated, depending on type and quality of restriction enzyme. Blunt ends: > 80% of the DNA is ligated, depending on type and quality of restriction enzyme.
Inactivation of enzyme
T4 DNA Ligase* can be completely inactivated by a 10 min incubation at 65C. Heat inactivation should only be applied if the ligation reaction mixture is used in experiments other than transformation assays. Otherwise, a drastic decrease of (> factor 20) transformants is possible.
* Product available from Roche Applied Science (Cat. No. 10 481 220 001 1000 U; Cat. No. 10 716 359 001 500 U)
Working with DNA
22
1.5.
Cloning of DNA
Dephosphorylation with rAPid Alkaline Phosphatase
Properties
Catalyzes the dephosphorylation of 5-protruding, 5-recessive and 5 blunt ends from ssDNA, dsDNA, ssRNA and dsRNA. rAPid Alkaline Phosphatase catalyzes the dephosphorylation of 5' phosphates from DNA and RNA, nucleotides, and proteins. Is active in restriction enzyme buffers; therefore, restriction enzyme digestion, dephosphorylation, enzyme inactivation, ligation, or 5'-end labeling can be performed without purification steps. 0.5 M Tris, 50 mM MgCl2, pH 8.5 at 20C. Buffer is stable at 15 to 25C. Unlike calf intestinal phosphatase, rAPid Alkaline Phosphatase is rapidly, completely, and irreversibly inactivated by heat treatment for two minutes at +75C. It is therefore an excellent alternative to Shrimp Alkaline Phosphatase. The total procedure including restriction enzyme digestion, dephosphorylation, enzyme inactivation and ligation can be performed in one single tube by using Roche Applied Sciences Rapid DNA Dephos & Ligation Kit (Cat. No. 04 898 117 001)
Dephosphorylation buffer, 10 x Inactivation of enzyme
Standard Assay: Dephosphorylation of 5ends of dsDNA fragments to prevent self-annealing of vector DNA prior to the insertion of DNA fragments.
Components Template DNA 10 x rAPid Alkaline Phosphatase buffer, 10x conc. rAPid Alkaline Phosphatase H2 O Incubation recessive or protruding ends 1 pmol 2 l 1 unit Add up to 20 l 10 min at 37C blunt ends 0.2 pmol 2 l 1 unit Add up to 20 l 30 min at 37C
Working with DNA
23
1.5.
5P 3OH 5P 3OH
Cloning of DNA
Modifying sticky ends to blunt ends: 5protruding and 3recessed ends: C A G 3OH G T C T T A A 5P C A G 3OH G T C T T A A G 5P
Klenow 5P 3OH 5P 3OH T4 DNA Polymerase
C A G A A T T 3OH G T C T T A A 5P C A G 3OH G T C 5P
T7 DNA Polymerase Mung Bean Nuclease
Fill-in 3recessed ends
Remove 5protruding ends
Modifying sticky ends to blunt ends: 3protruding and 5recessed ends:

5P 3OH 5P 3OH
A G C T G C A 3OH T C G 5P A G C T G C A 3OH T C G 5P
Klenow
5P 3OH 5P 3OH T4 DNA Polymerase
A G C T G C A 3OH T C G A C G T 5P A C G 3OH T C G 5P
T7 DNA Polymerase Mung Bean Nuclease
Fill-in 5recessed ends
Remove 3protruding ends
Working with DNA
24
1.5.
Cloning of DNA
Klenow* for partial or complete filling of 3recessed ends
Properties
DNA dependent 5-3polymerase with 3-5exonuclease activity catalyzing the addition of mononucleotides from dNTPs to the 3OH terminus of a primer/template DNA.
G 3OH C T T A A 5P A 3OH T T C G A 5P
3OH
5P 3OH 5P 3OH 5P 3OH
dATP dTTP
5P 3OH
G A A T T 3OH C T T A A 5P A A G C T 3OH T T C G A 5P G A 3OH C T A G 5P
dNTP dATP dGTP
5P 3OH 5P 3OH
C T A G 5P
Filling buffer, 10 x
500 mM Tris (pH 7.5), 100 mM MgCl2, 10 mM DTT, 500 g/ml BSA. Buffer is stable at 15 to 25C, store in aliquots.
Standard Assay: Partial or complete filling of 3recessed ends.

Components Template DNA Nucleotides*, final concentration 10 x Filling buffer Klenow* H2 O Incubation Complete filling 1 g DNA 1 mM of desireda dNTPs each 2 l 1 unit Add up to 20 l 15 min at 37C Partial filling 1 g DNA 1 mM of desireda dNTPs each 2 l 1 unit Add up to 20 l 15 min at 37C
Add 2 l 0.2 M EDTA and/or heat to 65C for 10 min.
* Products available from Roche Applied Science (Klenow: Cat. No. 11 008 412 001 500 U; Cat. No. 11 008 404 001 100 U; Set of dNTPs, PCR-Grade: Cat. No. 11 969 064 001 4 x 250 l (25 mol); Cat. No. 03 622 614 001 4 x 1,250 l (125 mol).
a
Note: Please only add the desired dNTPs as needed according to the sequence.
Working with DNA
25
1.5.
Cloning of DNA
Mung Bean Nuclease for removing of 3and 5protruding ends
Properties
Degrades ssRNA and ssDNA to produce 5-phosphoryl oligo- and mononucleotides. dsDNA, dsRNA and DNA: RNA hybrids are relatively resistant to the enzyme.
3OH 5P 3OH 5P 3OH 3OH 5P 3OH 5P
5P
A A T T C
3OH 5P
C T T A A 5P T G C A 3OH
5P
3OH
A C G T
Nuclease buffer, 10x
300 mM sodium acetate, pH 4.6, 500 mM NaCl, 10 mM zinc acetate, 0.01% Triton X-100. Buffer is stable at 15 to 25C, store in aliquots
Standard Assay: Removing 5 and 3protruding ends of DNA creating blunt ends.
Components Template DNA 10 x Nuclease buffer Mung Bean Nuclease H2 O Incubation Removing ends 1 g DNA 10 l 5 units Add up to 100 l 1 hour at 25C
Add EDTA to a final concentration of 1 mM or SDS to a final concentration of 0.01%.
Working with DNA
26
1.5.
Cloning of DNA
Miscellaneous
Competent cells and transformation
For an overview of the different procedures, please refer to Hanahan, D. (1983) Studies on transformation of E. coli with plasmids. J. Mol. Biol. 166, 557579 Hanahan, D. et al. (1991) Plasmid tranformation of E. coli and other bacteria. Methods in Enzymology 204, 63113 Hengen, P. N. (1996) Methods and reagents, Preparing ultra-competent Escherichia coli. Trends in Biochemical Sciences 21(2), 7576 Ready-to-use competent cells are available from different suppliers commercially. A wide variety of different cloning systems and kits are available from different suppliers. Roche Applied Science offers three systems: PCR Cloning Kit (Cat. No. 11 939 645 001): for cloning blunt-end PCR products up to 10 kb Expand Cloning Kit (Cat. No. 11 940 392 001): for cloning blunt-end PCR products from 7 to 36 kb
Commercially available cloning kits
Rapid DNA Dephos & Ligation Kit (Cat. No. 04 898 117 001): enabling ligation of sticky and blunt-end fragments within 5 minutes. Please refer to reference 6 (page 175191) for a complete overview.
Commonly used bacterial strains
Strain BL21 C600e DH5 HB101 JM108 JM109 JM110
Genotype E. coli B F- dcm ompT hsdS(rB- mB-) gal (Studier, F.W. et al (1986) J. Mol. Biol., 189, 113.) supE44 hsdR2 thi-1 thr-1 leuB6 lacY1 tonA21; (Hanahan, D. (1983) J. Mol. Biol. 166, 557.) supE44 (lacU169 (80dlacZM15) hsdR17 recA1 endA1 gyrA96 thi-1 relA1; (Hanahan, D. (1983) J. Mol. Biol. 166, 557.) supE44 hsdS20 recA13 ara-14 proA2 lacY1 galK2 rpsL20 xyl-5 mtl-1; (Hanahan, D., (1983) J. Mol. Biol. 166, 557.) recA1 supE44 endA1 hsdR17 gyrA96 relA1 thi (lac-proAB); (Yanisch-Perron, C. et al., (1985) Gene 33, 103.) recA1 supE44 endA1 hsdR17 gyrA96 relA1 thi (lac-proAB) F[traD36proAB+, lacIq lacZM15]; (Yanisch-Perron, C. et al., (1985) Gene 33, 103.) rpsL (Strr) thr leu thi-l lacY galK galT ara tonA tsx dam dcm supE44 (lac-proAB) F[traD36proAB+, laclq lacZM15]; (Yanisch-Perron, C. et al., (1985) Gene 33, 103.)
Working with DNA
27
1.5.
Cloning of DNA
Commonly used bacterial strains (continued)
Strain K802
Genotype supE hsdR gal metB; (Raleigh, E. et al., (1986) Proc.Natl. Acad.Sci USA, 83, 9070.; Wood, W.B. (1966) J. Mol. Biol., 16,118.) recB recJ sbc C201 uvrC umuC:Tn5(kanr) lac, (hsdRMS) endA1 gyrA96 thi relA1 supE44 F[proAB+ lacIq lacZM15 Tn10 (tetr); (Greener, A. (1990) Strategies, 3, 5.) supE hsd 5 thi (lac-proAB) F[traD36proAB+, lacIq lacZM15]; (Gibson, T.J. (1984) PhD Theses. Cambridge University, U.K.) supE44 hsdR17 recA1 endA1 gyrA46 thi relA1 lac F[proAB+, lacIq lacZM15 Tn10 (tetr) ]; (Bullock et al., (1987) BioTechniques, 5, 376.)
SUREr
TG1
XL1-Bluer
Commonly used E. coli strains
For a detailed overview on the genotypes and references of the most commonly used E. coli strains, please refer to Molecular Biology LABFAX, edited by T.A. Brown, Bios scientific publishers, ISBN 1 872748 00 7.
Notes
Working with DNA
28
1.6.
Labeling of DNA and Oligonucleotides

General Considerations
Template
The higher the purity of the DNA template, the better the labeling efficiency. For the random primed DNA labeling method, it is critical that the template is linearized and completely heat-denatured prior to the labeling reaction. The choice of labeling method depends on: the type of application (e.g., Southern, Dot Blot, ) the available template (e.g., cloned insert, oligonucleotide, ) the requested sensitivity (e.g., single copy gene detection, ) The table on page 30 gives an overview of the different methods and their sensitivity for a given application. Unincorporated labeled nucleotides should be removed from the labeling mix: removal from DNA fragments via the High Pure PCR Product Purification Kit* (Cat. No. 11 732 676 001 up to 250 purifications) or the High Pure PCR Cleanup Micro Kit (Cat. No. 04 983 955 001 up to 50 purifications) or via ethanol precipitation. removal from oligonucleotides: via ethanol precipitation with glycogen* (20 g/reaction) or Quick Spin columns*. This enables a more accurate quantification of the incorporated label and reduces background in hybridization experiments.
Choice of labeling method
Purification of labeled probe
* Products available from Roche Applied Science
Type of label
Several non-radioactive methods have been developed. The use of these labels (e.g., digoxigenin, biotin, fluorescein, ) offer several advantages: The technology is safe and highly sensitive Results can be achieved much faster (in minutes rather than in hours or days) Probes can be stored for a longer period of time compared to radioactive probes Hybridization solutions can be reused several times For an overview of the non-radioactive systems available from Roche Applied Science, please refer to reference 3, 10 and 14.
Note: For detailed information concerning labeling and detection of DNA and RNA please visit: http://www.roche-applied-science.com/dig
Working with DNA
29
1.6.

Overview of different techniques Labeling Methods Random Primed Labeling PCR labeling 5 End labeling 3 End labeling Relative sensitivity +++ +++ ++ ++ +++ +++ +++ +++
Application Southern Blotting Northern Blotting
Dot/Slot Blotting
Random Primed Labeling PCR labeling 5 End labeling 3 End labeling
Application Colony/Plaque hybridisation
Labeling Methods Random Primed Labeling PCR labeling 5 End labeling 3 End labeling
Relative sensitivity +++ +++ +++ +++ +++ ++ ++ ++
In Situ Hybridisation
PCR labeling 5 End labeling Nick Translation 3 End labeling
Working with DNA
30
Is your TARGET DNA or RNA?
RNA
DNA
DIG Northern Starter Kit* Cat. No. 12 039 672 910

Is your PROBE DNA, RNA, or OLIGO? RNA
DIG RNA Labeling Kit (SP6/T7) Cat. No. 11 175 025 910 DIG RNA Labeling Mix Cat. No. 11 277 073 910
Note: RNA probes are recommended for detecting low-abundance mRNA.
RNA
Is your PROBE DNA, RNA, or OLIGO?
DNA Is the Oligonucleotide already synthesized?
OLIGO (Recommended only for abundant targets) OLIGO (Recommended only for abundant targets)
DNA
YES
Do you want to use PCR or Random Primed Labeling?
DIG Oligonucleotide 3End Labeling Kit, 2nd generation Cat. No. 03 353 575 910 DIG Oligonucleotide Tailing Kit, 2nd generation Cat. No. 03 353 583 910
Do you want to use PCR or Random Primed Labeling?
DIG Labeling of Nucleic Acids
PCR
PCR DIG Probe Synthesis Kit Cat. No. 11 636 090 910 DIG-High Prime DNA Labeling and Detection Starter Kit II* Cat. No. 11 585 614 910 DIG-High Prime Cat. No. 11 585 606 910
PCR
RPL
RPL
DIG DNA Labeling Kit Cat. No. 11 175 033 910
*Note: These kits include labeling reagents and detection substrate.
1.6.
Do you want chemiluminescent or colorimetric visualization? Chemiluminescent Colorimetric
Do you want individual reagents or convenient detection kits? Reagents Reagents
Do you want individual reagents or convenient detection kits?
Kits
CDP-Star, ready-to-use Cat. No. 12 041 677 001

Kits
NBT/BCIP Stock Solution Cat. No. 11 681 451 001 NBT/BCIP, ready-to-use Tablets Cat. No. 11 697 471 001
CSDP, ready-to-use Cat. No. 11 755 633 001
DIG Luminescent Detection Kit Cat. No. 11 363 514 910 DIG-High Prime DNA Labeling and Detection Starter Kit II* Cat. No. 11 585 614 910 DIG Northern Starter Kit* Cat. No. 12 039 672 910
* Note: These kits include labeling reagents and detection substrate.
DIG Nucleic Acid Detection Kit, Colorimetric Cat. No. 11 175 041 910 DIG-High Prime DNA Labeling and Detection Starter Kit I* Cat. No. 11 745 832 910
For a complete overview, please refer to references 3, 10 and 14 thus visit: http://www.roche-applied-science.com/dig
Working with DNA
31
1.6.

Random Primed Labeling with Klenow
Principle
Based on the random hybridization of a mixture of all possible hexanucleotides to the ssDNA form of the DNA that needs to be labeled. The complementary strand is synthesized from the 3OH termini of the hexanucleotide primers using the 5-3polymerase activity of Klenow
5P 3OH 3OH 5P
5P 3OH * Incorporation of 5P 1. Non-radioactive nucleotides: digoxigenin, biotin, fluorochromes 2. Radioactive nucleotides: 3OH [32P], [35S], [3H]
Denature, anneal random hexanucleotides
3OH
5P
Labeling buffer, 10 x Application and typical results
500 mM Tris (pH 7.2), 100 mM MgCl2, 1 mM DTT and 2 mg/ml BSA Buffer is stable at 15 to 25C, store in aliquots. DNA is denatured by heating for 10 min at 95C and immediately put on ice
Klenow Enzyme + dNTP*
3OH
5P
Standard assay prepare reaction mix on ice :

Components Template DNA Nucleotides, final concentration Labeled nucleotide, final concentration 10 x Hexanucleotide mix (62.5 A260 units/ml) Klenow enzyme 10 x Labeling buffer H2 O Incubation Non-radioactive 10 ng 3 g DNA 100 M of dATP, dCTP, dGTP each, 65 M dTTP 35 M DIG-, Biotin- or ** Fluorochrome-dUTP 2 l 2 units 2 l Add up to 20 l at least 60 min at 37C Radioactive* 10 ng 2 g DNA 25 M of dATP, dGTP, dTTP each [32P]dCTP (3,000 Ci/mmol), 50 Ci (1.85 MBq) 2 l 2 units 2 l Add up to 20 l 30 min at 37C
Size of DNA fragment to be labeled: from 200 up to 50,000 bp. Size of labeled DNA fragment ranges from 80 200 bp.
Inactivation of enzyme Tip
Add 2 l 0.2 M EDTA (pH 8.0) and/or heat to 65C for 10 minutes. Do not solubilize the DNA to be labeled in buffers containing EDTA since EDTA inhibits the reaction. Optimized kits (e.g., Random Primed DNA Labeling Kit Cat. No. 11 004 760 001) are available from Roche Applied Science.
** For a complete overview, please refer to references 10 and 14.
Working with DNA
32
1.6.

Nick Translation with DNA Polymerase I and DNAse I
Principle
Based on the ability of DNAse I to introduce random nicks in dsDNA at low enzyme concentrations and in the presence of Mg2+. The E. coli DNA Polymerase I synthesizes DNA complementary to the intact strand in the 5-3direction using the 3OH termini of the nicks as primers. The 5-3exonuclease activity of the enzyme simultaneously removes nucleotides in the direction of synthesis that are replaced by nucleotides supplemented to the reaction.
First nucleotide on the 5-phosphate side of the nick has been removed Replacement of removed nucleotide by labeled dNTP*
A nick with a 3-OH terminus

5P 3OH
nick
5P 3OH
3OH 5P
5P 3OH
3OH 5P
3OH 5P
Moving of the nick towards the 3-terminus
nick
5P 3OH
3OH 5P
* Incorporation of
1. Non-radioactive nucleotides: digoxigenin, biotin, fluorochromes 2. Radioactive nucleotides: [32P], [35S], [3H]
NT Buffer, 10 x
500 mM Tris (pH 7.4), 100 mM MgCl2, 10 mM DTT, 500 g/ml BSA. Buffer is stable at 15 to 25C, store in aliquots.
Standard Assay prepare reaction mix on ice:

Components Template DNA Nucleotides, final concentration Labeled nucleotide, final concentration Mixture of DNA Polymerase I and DNAse Ia 10 x NT buffer H2 O Incubation Non-radioactive 30 ng 2 g 100 M of dATP, dCTP, dGTP each, 60 M dTTP 40 M DIG-, Biotin- or ** fluorochrome-dUTP 2 l 2 l Add up to 20 l 90 min at 15C Radioactive* 30 ng 2 g 20 M of dATP, dGTP, dTTP each [32P]dCTP (3,000 Ci/mmol), 20 Ci (0.74 MBq) 2 l 2 l Add up to 20 l 30 min at 15C
* An incorporation rate of > 65% (~3 x 10 8 dpm/g) is obtained after 30 min. a The ratio of DNA Polymerase I versus DNAse I determines the efficiency of the reaction. A special optimized mixture is available from Roche Applied Science.
Size of DNA fragment to be labeled: from 400 bp to 800 bp.

Add 2 l 0.2 M EDTA (pH 8.0) and/or heat to 65C for 10 minutes. Premixed Nick Translation mixes (e.g., Cat. No. 11 745 808 910) and different kit systems (Cat. No. 10 976 776 001) are available from Roche Applied Science.
** For a complete overview, please refer to references 10 and 14.
Working with DNA
33
1.6.

3End labeling with Terminal Transferase
Principle
Catalyzes the template independent addition of dNTPs or ddNTPs to the 3OH ends of ds and ssDNA and oligonucleotides.
dNTP 5P 3OH ddNTP 5P pNpNpN3OH 5P pN3H
dNTP 5P 3OH 3OH 5P ddNTP
5P 3OHpNpNpN 5P 3HpN
pNpNpN3OH 5P pN3H 5P
incorporation of Non-radioactive deoxy- or dideoxynucleotides: digoxigenin, biotin, fluorochromes Radioactive deoxy- or dideoxynucleotides: [32P]
Transferase buffer, 10 x
2 M potassium cacodylate, 250 mM Tris, 2.5 mg/ml BSA, pH 6.6 at 25C. Buffer is stable at 15 to 25C, store in aliquots.

Components Template DNA Radioactive nucleotides, final concentration Non-radioactive nucleotides, final concentration Tailing with dNTPs 10 to 100 pmol 3ends [32P]dNTP (3000 Ci/mmol), 50 Ci (1.85 MBq) 50 M Dig, Biotin or fluorochrome dUTP mixed with 500 M dATP* 6.25 M of dATP or dTTP* 5 M of dGTP or dCTP* A or T Tails: 1.5 mM G or C Tails: 0.75 mM 400 units 2 l Add up to 20 l 15 min at 37C 3 End labeling with ddNTPs 10 to 100 pmol 3ends [32P]ddNTP (3000 Ci/mmol), 50 Ci (1.85 MBq) 50 M Dig, Biotin or fluorochrome dUTP
CoCl2 Terminal Transferase* 10 x transferase buffer H2 O Incubation
5 mM 400 units 2 l Add up to 20 l 15 min at 37C
* For more information on length of tail, type of tail (homo- or heteropolymeric), please refer to reference 10.
Add 2 l 0.2 M EDTA (pH 8.0) and/or heat to 75C for 10 minutes. DIG Tailing and DIG 3End Labeling kits are available from Roche Applied Science.
Product available from Roche Applied Science: Terminal Transferase, recombinant (Cat. No. 03 333 574 001 24,000 U; Cat. No. 03 333 566 001 8,000 U)
Working with DNA
34
1.6.

5End labeling with Polynucleotide Kinase
Principle
Catalyzes the transfer of the terminal phosphate group of ATP to the 5OH termini of ds and ssDNA and RNA. Catalyzes the exchange of terminal 5P groups of ds and ssDNA and RNA. Catalyzes the removal of phosphate groups from the 3termini of ds and ssDNA and RNA.
5OH 3OH 5P 3OH 5P 3P APPP APP 5P 3OH 5P 3OH 5P 3OH
Phosphorylation buffer,10 x Exchange buffer, 10 x
500 mM Tris, 100 mM MgCl2, 1 mM EDTA, 50 mM dithiothreitol, 1 mM spermidine, pH 8.2 at 25C. Buffer is stable at 15 to 25C, store in aliquots. 500 mM Imidazole-HCl, 100 mM MgCl2, 1 mM EDTA, 50 mM dithiothreitol, 1 mM spermidine, 3 mM ADP, pH 6.6 at 25C. Buffer is stable at 15 to 25C, store in aliquots.

Components Template DNA nucleotides, final concentration Polynucleotide Kinase buffer H2 O Incubation Phosporylation of 5OH groups 20 pmol 5OH ends 20 pmol [32P]ATP 10 units 2 l, Phosphorylation buffer,10 x Add up to 20 l 30 min at 37C
32
Exchange of 5P groups 20 pmol of 5P termini 40 pmol [32P]ATP 10 units 2 l, Exchange buffer, 10 x Add up to 20 l 30 min at 37C
Phosphorylation: More than 30% of [ P] from [32P]ATP is incorporated. Exchange: More than 10% of [32P] from [32P]ATP is incorporated.
Stop phosphorylation and exchange reaction by putting the sample on ice. A special Polynucleotide Kinase, lacking the 3phosphatase activity is available from Roche Applied Science (Cat. No. 10 709 557 001 200 U; Cat. No. 10 838 292 001 1,000 U).
Working with DNA
35
1.7.
Sources
Amplification of DNA
Avoiding Contamination
Laboratory benches, equipment and pipetting devices can be contaminated by previous DNA preparations, plasmid DNA or by purified restriction enzyme fragments. Cross-contaminations between samples during isolation of nucleic acids. Products from previous PCR amplifications. Use sterile techniques and always wear fresh gloves. Always use new and/or sterilized glassware, plasticware and pipettes to prepare the PCR reagents and template DNA. Sterilize all reagents and solutions by filtration through a 0.22 m filter. Have your own private set of PCR reagents and solutions and use them only for PCR reactions. Store these reagents in small aliquots. Always include a negative (all reaction components without DNA) and a positive control (e.g., a PCR that has been successfully used in previous experiments).
Sample handling
Laboratory facilities
Set up physically separated working places for template preparation setting up PCR reactions post-PCR analysis Use dedicated (PCR use only) pipettes, micro-centrifuges and disposable gloves. Use aerosol resistant pipette tips. Set up a PCR reaction under a fume hood (with UV light).
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36
1.7.
Purity
Reaction Components: Template
The purity of the template largely influences the outcome of the PCR. Large amounts of RNA in the sample can chelate Mg2+ and reduce the yield of the PCR. Impure templates may contain inhibitors (organic substances: phenol, chloroform, ethanol) that decrease the efficiency of the reaction. Always use a purification product and/or procedure specially designed to purify DNA for PCR reactions (see page 7). Template DNA should be of high molecular weight. To check the size and integrity of the DNA, run an aliquot on an agarose gel. The amount of template in a reaction strongly influences the performance of the PCR. The recommended amount of template for a standard PCR is maximum 500 ng of human genomic DNA 1 10 ng of bacterial DNA 0.1 500 ng of plasmid DNA The optimal amount of template depends on the application and the allowed error rate within the amplified DNA: the lower the amount of template, the higher the cycle number and the higher the probability for errors within the amplified DNA.
Integrity Amount
Lower amounts of template will require specific reaction modifications like changes in cycle numbers, redesign of primers, etc.
Tip
When testing a new template, include a positive control with primers that amplify a product of about the same size and produce a good yield. Avoid to dissolve the template in TE buffer since EDTA chelates Mg2+. Use 510 mM Tris (pH 7 8) or water to dissolve the template.
Working with DNA
37
1.7.
General
Reaction Components: Primers
Length: 18 to 24 nucleotides. GC content: 40 60%, with a balanced distribution of G/C and A/T rich domains. Contain no internal secondary structure. Are not complementary to each other at the 3ends to avoid primer-dimer forming. Estimation of melting temperature Tm: Tm = [2C x (number of A and T bases)] + [4C x (number of G and C bases)] see page 164 (Chapter 6.2. Formulas to calculate melting temperature) for more information. Design primers with similar Tm values. Optimal annealing temperatures are ~ 5 to 10C lower than the Tm values of the primers and have to be determined empirically. Design primers as such that an annealing temperature of 55 65C is allowed, for maximum specificity, use temperatures of 62 72C.
Melting temperature
Annealing temperature
Concentrations of primers
Concentrations between 0.1 and 0.6 M are generally optimal. Refer to page 39 to convert M values into pmol values of primers. Higher concentrations may promote mispriming and accumulation of non-specific products. Lower concentrations may be exhausted before the reaction is completed, resulting in lower yields of the desired product. Stock solutions: dissolve lyophilized primers in a small volume of 5 mM Tris, pH 7.5 and store at 15 to 25C. Working solution: to avoid repeated freezing and thawing, prepare small aliquots of 10 pmol/l and store at 15 to 25C. When testing new primers, include a positive control reaction with a template that has been tested in PCR.
Storage
Tip
Working with DNA
38
1.7.
Reaction Components: Oligonucleotides: Commonly used Formulas
Concentration Molecular Weight (in Dalton)
1 A260 Unit of an Oligonucleotide: 20 30 g/ml H2O MW = (N A x 312.2) + (N G x 328.2) + (N C x 288.2) + (NT x 303.2) + P N X = number of residues of respective nucleotide in the oligonucleotide P = + 17 for phosphorylated oligonucleotide P = 61 for dephosphorylated oligonucleotide
pmol of oligo = g (of oligo) x 10 6 pg 1 g x 1 pmol 1 g (of oligo) x 3,030 x = 330 pg N N
Conversion of g to pmol
e.g., 1 g of a 20 bases oligo = 151.5 pmol

Conversion of pmol to g g of oligo = pmol (of oligo) x 330 pg 1 g x x N = 1 pmol 10 6 pg
= pmol (of oligo) x N x 3.3 x 10-4
e.g., 1 pmol of a 20 bases oligo = 0.0066 g

N = number of bases
Conversion of M to pmol
1 l of a X M primer solution = X pmol primers example: Question: given primer solution: 2.5 M amount of primers needed for experiment: 2 pmol Answer: 1 l of a 2.5 M primer solution = 2.5 pmol 2 pmol = 0.8 l 1 l of a X pmol/l primer solution = X M primers example: Question: given primer solution: 20 pmol/l amount of primers needed for experiment: 5 M Answer: 1 l of a 20 pmol/l primer solution = 20 M primers 5 M = 0.25 l
Conversion of pmol to M
Working with DNA
39
1.7.
Software
Software*
Sample of web sites that provides tutorials, lectures and tips on primer design: Primer design software: http://www.premierbiosoft.com http://www.universalprobelibrary.com http://molbiol-tools.ca/PCR.htm Calculating Tm for a given primer: http://www.roche-applied-science.com/benchmate
* Web sites continually appear, disappear and change addresses, quickly invalidating any list of useful sites. All of the web sites given here were operating in May, 2007.
Reaction Components: MgCl2 concentration Function of Mg2+ ions Concentration of Mg2+ ions
Mg2+ ions form soluble complexes with dNTPs and template DNA to produce the actual substrate that the polymerase recognizes. The concentration of free Mg2+ ions depends on the concentrations of compounds like dNTPs, free pyrophosphates (PPi) and EDTA (e.g. from TE buffer). These compounds bind to the ions via their negative charges. Therefore, the concentration of Mg2+ should always be higher than the concentration of these compounds. The most optimal concentration should be determined empirically and may vary from 1 mM to 5 mM. The most commonly used MgCl2 concentration is 1.5 mM, with a dNTP concentration of 200 M each. Excess Mg2+ in the reaction can increase non-specific primer binding and increase the non-specific background of the reaction. Too little Mg2+ in the reaction can result in a lower yield of the desired product. A PCR Optimization Kit (Cat. No. 11 636 138 001) available from Roche Applied Science allows an easy and straightforward optimization of this reaction component
Tip
Working with DNA
40
1.7.
Reaction Components: dNTP concentration
Concentration of dNTP
Always use balanced solutions of all four dNTPs to minimize the error rate. The final concentration of each dNTP should be between 50 and 500 M, the most commonly used concentration is 200 M. Increase concentration of Mg2+ when increasing the concentration of dNTPs. Increases in dNTP concentrations reduces the concentration of free Mg2+ thereby interfering with the activity of the polymerase enzyme. For carry-over prevention, dTTP is substituted by dUTP. A three times higher concentration of dUTP (e.g., 600 M) compared with the other nucleotides normally results in a good amplification. For more information on this technique, please refer to reference 6. Store stock solutions at 15 to 25C. Working solutions (e.g., 100 l mixture of 10 mM of each nucleotide) are also stored at 15 to 25C. Special PCR grade nucleotides* available from Roche Applied Science are specially purified and tested to ensure optimal results and maximum sensitivity in all PCR applications.
Storage
Tip
* see reference 7.
Reaction Components: Choice of Polymerase (see also reference 6)

Difcult Template PCR Hot Start PCR Basic PCR
Length 35 kb 30 kb 25 kb 20 kb 15 kb 10 kb 5 kb 3 kb 1 kb
High Fidelity PCR
Long Range PCR
Specicity Sensitivity Robustness Accurracy* Carryover Prevention Master Mix available
1x yes yes
Taq DNA Polymerase
4x yes no
FastStart High Fidelity PCR System
3x no no
GC-RICH PCR System
18 x no yes
Pwo SuperYield DNA Polymerase
6x yes yes
Expand High FidelityPLUS PCR System
3x no no
Expand Long Template PCR System
2x no no
Expand 20kbPLUS PCR System
yes yes
FastStart Taq DNA Polymerase
* compared to Taq DNA Polymerase
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41
1.7.
Reaction Components: Hot Start Techniques
Principle
Taq DNA Polymerase has a low activity at temperatures used to mix the different reaction components (e.g., at room temperature or at 4 C). At these temperatures, the primers may anneal non-specifically and the polymerase may elongate these primers prior to the initial cycle resulting in a series of non-specific amplification products. The hot start technique prevents these non-specific products. Manual: 1 component such as the polymerase or Mg2+ - is only added to the reaction tube after the temperature is > 70 C. Polymerase Antibodies: The polymerase is inactivated by a heat-sensitive antibody. As the temperature rises in the tube, the antibody is inactivated, setting the active polymerase free. Chemical Modification of Polymerases: Addition of heat-labile blocking groups to some amino acids renders the Taq DNA Polymerase inactive at room temperature. At higher temperatures, these blocking groups are removed and the enzyme is activated (e.g., FastStart Taq DNA Polymerase (Cat. No. 12 032 937 001) available from Roche Applied Science).
Techniques
Reaction Components: Other factors Concentration of Polymerase
For most assays, the optimal amount of thermostable DNA Polymerase or blend of polymerases is between 0.5 and 3.5 units per 50 l reaction volume. Increased enzyme concentrations sometimes lead to decreased specificity. In general, the pH of the reaction buffers supplied with the corresponding thermostable DNA Polymerase (pH 8.3 9.0) gives optimal results. For some systems, raising the pH may stabilize the template and improve the reaction. In some cases, the following compounds can enhance the specificity and/or efficiency of a PCR: Betaine (0.5 2 M) Bovine Serum Albumin (100 ng/50 l reaction mix) Dimethylsulfoxide (2 10%, v/v) Glycerol (1 5%, v/v) Pyrophosphatase (0.001 0.1 units/reaction) Spermidine, Detergents, Gelatine, T4 Gene 32 protein Formamide (2 10%)
pH
Reaction additives
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42
1.7.
Cycling Profile for standard PCR
Initial denaturation
It is very important to denature the template DNA completely by initial heating of the PCR mixture. Normally, heating for 2 minutes at 94 95C is enough to denature complex genomic DNA. If the template DNA is only partially denatured, it will tend to snap-back very quickly thereby preventing efficient primer annealing and extension, or leading to self-priming which can lead to false positive results. Denaturation at 94 95C for 20 to 30 seconds is usually sufficient but must be adapted for the thermal cycler and tubes being used. If the denaturation temperature is too low, the incompletely melted DNA snaps back, preventing efficient primer annealing and extension. Use a longer denaturation time or higher denaturation temperature for GC rich template DNA. Never use a longer denaturation time than absolutely required, unnecessary long denaturation times decreases the activity of the polymerase. The choice of the primer annealing temperature is a very critical factor in designing a high specificity PCR and for most purposes has to be optimized empirically (see page 38). If the temperature is too high, no annealing occurs.
Denaturation during cycling
Primer annealing
If the temperature is too low, non-specific annealing will increase dramatically. If the primers have complementary bases, primer dimer effects will occur.
Primer extension
For fragments up to 3 kb, primer extension is carried out at 72C. Taq DNA Polymerase adds approximately 60 bases per second at 72C. A 45 second extension is sufficient for fragments up to 1 kb. For extension of fragments up to 3 kb, allow about 45 seconds per kb. However, this may need to be adjusted for specific templates. To improve yield, use the cycle extension feature of the cycler: first 10 cycles: a constant extension time (e.g., 45 seconds for a 1 kb product) next 20 cycles: increase the extension time by 2 5 seconds per cycle (e.g., 50 seconds for cycle 11, 55 seconds for cycle 12, ...) this allows the enzyme more time to do its job because, as PCR progresses, there is more template to amplify and less active enzyme (due to denaturation of the protein during the prolonged high PCR temperatures) to perform the extension.
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43
1.7.
Cycling Profile for standard PCR (continued)
Cycle number
In an optimal reaction less than 10 template molecules can be amplified in less than 40 cycles to a product detectable by gel electrophoresis. Most PCRs should only include 25 35 cycles. As cycle number increases, non-specific products can accumulate. Usually, after the last cycle, the reaction tubes are held at 72C for 5 15 minutes to promote completion of partial extension products and annealing of single-stranded complementary products. After the final extension, immediately put the samples on ice or store at 4C.
Final extension
1.7.
Mix 1
Standard Pipetting Scheme
(for 1 reaction):
Final concentration variable Each dNTP, 200 M 0.1 0.6 M each 0.1 0.25 g
Mix 2
(for 1 reaction):
Taq PCR 19.75 l 5 l 0.25 l 25 l 1x 1.25 units Final concentration
Reagent H2 0 10 mM PCR Nucleotide Mix 1 l Upstream and downstream primer Template DNA Volume variable variable 25 l
Reagent H2 0 Enzyme buffer, 10 x conc Enzyme (5U/l) Volume
Combine mix 1 and 2 in a thin-walled PCR tube. Gently vortex the mixture to produce a homogenous reaction, then centrifuge briefly to collect the sample at the bottom of the tube. Standard pipetting scheme applies for enzymes like Taq DNA Polymerase, and Tth DNA Polymerase, and Pwo SuperYield DNA Polymerase.
Working with DNA
44
Standard PCR Temperature Profile

Profile A: Temperature Initial denaturation Denaturation Annealing Elongation Final elongation 94C 94C 50 65Ca 72C 72C Time 2 min 15 30 s 30 60 s 45 s 3 min 7 min 25 30 Cycle number Initial denaturation Denaturation Annealing Elongation Denaturation Annealing Elongation Final elongation
a The
Profile B*: Temperature 94C 94C 50 65Ca 72C 94C 50 65Ca 72C 72C Time 2 min 15 30 s 30 s 45 s 3 min 15 30 s 30 s* 45 s 3 min +5 added seconds/cycle 7 min Cycle number
10
15 20
exact annealing temperature depends on the melting temperature of the primers * This profile ensures a higher yield of amplification products
Notes
Working with DNA
45
1.8.
Quantitative Real-Time PCR

Methods
Introduction
Due to its sensitivity and dynamic range, PCR is the ideal technique to quantify nucleic acids. Traditionally, the quantification of a given nucleic acid of interest was determined by methods such as: competitive PCR, PCR ELISA, limiting dilution PCR, radioactive methods. These methods are based upon end-point analysis and have several limitations.
End-point analysis
N: number of amplified molecules n: number of amplification cycles
The figure above shows typical amplification curves. Each curve has 3 segments: Background phase. Exponential - or log-linear - phase Plateau phase End-point analysis is not very suitable for quantitative PCR because it is done in the "plateau phase" of PCR where the reaction no longer follows exponential kinetics. In this phase, the reaction can no longer be described by a mathematical formula. Thus, it is not possible to directly correlate the end-point signal with the initial template amount or target copy number. Further, in the plateau phase, PCR efficiency decreases steadily, because reaction compounds are being consumed and inhibitors are accumulating. These effects vary from sample to sample, resulting in different end-point signals.
Real-Time PCR
Real-time PCR offers an alternative method for both qualitative and quantitative analysis. This type of analysis allows the amplification and fluorescent detection steps to be performed by a single instrument in a single tube with data recorded online. A real-time PCR instrument measures the accumulation of PCR products during amplification with fluorescent dyes. Because PCR itself and the detection of PCR products occur in the same reaction (vessel), this set-up is also called "homogeneous PCR". 46
Working with DNA
1.8.

Instrument-based Systems
Principles of Real-Time PCR LightCycler System
Simultaneous amplification and detection of specific nucleic acid sequences via fluorescence-detecting thermocyclers. The LightCycler System incorporates several features that make it the ideal tool for qualitative and quantitative PCR as well as mutation analysis in general laboratory applications. It includes instrumentation, software, reagents, technical support, and application-specific kits. Two real-time PCR systems are available from Roche Applied Science: The Carousel-based LightCycler Real-Time PCR System (LightCycler 2.0 Instrument, Cat. No.: 03 531 414 201). The LightCycler 2.0 Instrument is optimized for two fluorescence detection formats: SYBR Green I and HybProbe probes. In addition, the instrument supports a wide variety of other fluorescence detection formats, such as monocolor SimpleProbe probes, hydrolysis probes, and other formats based on FRET (fluorescence resonance energy transfer).
The LightCycler 480 thermal block cycler for either 96- or 384-well plates (LightCycler 480 Instrument, Cat. No.: 04 640 268 001 96 well, Cat. No.: 04 545 885 001 384 well). The LightCycler 480 System setup enables the use of all current generic DNA dyes (e.g., SYBR Green I, High Resolution Melting dye) and probes (HybProbe probes, SimpleProbe probes, Hydrolysis probes). For details concerning instrument, reagents and software please refer to http://www.lightcycler.com and www. lightcycler480.com.
Working with DNA
47
1.8.

Real-Time PCR Assay Formats
All real-time PCR systems detect a fluorescent dye, and then correlate this fluorescence signal to the amount of PCR product in the reaction. There are several methods for detecting and evaluating PCR products fluorimetrically. The most commonly used fluorescent assay methods fall into two classes, sequence-independent detection assays and sequence-specific probe binding assays. Each has its uses and its limitations.
SYBR Green I Hybridization Probes SimpleProbe Probes Hydrolysis Probes
Double stranded [ds] - specific intercalating dye. The presence of a specific amplification product is quantitatively recorded by an increase in fluorescence. Single-label probe with fluorescein. TaqMan technology using, e.g., FAM, HEX, or VIC.
Notes
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48
1.8.

Sequence-Independent Detection Assays
SYBR Green I Format
Sequence-independent assays rely on fluorophores (typically SYBR Green I) that bind to all doublestranded DNA molecules regardless of sequence. When the SYBR Green I dye intercalates into dsDNA, its fluorescence greatly increases. During the different stages of PCR, the intensity of the fluorescent signal will vary, depending on the amount of dsDNA that is present.
During annealing, PCR primers hybridize to the target and form small regions of dsDNA where SYBR Green I intercalates; the fluorescent signal slightly increases.
A
In the elongation phase, more dsDNA is formed and more SYBR Green I dye can intercalate; higher fluorescent signal.
At the end of the elongation phase, all DNA has become double-stranded and the maximum amount of SYBR Green I is intercalated. The fluorescence is measured (530 nm) at the end of each elongation phase.
Working with DNA
49
1.8.

Sequence-Specific Probe Binding Assays
FRET Principle
Sequence-specific assays rely on oligonucleotide probes that hybridize to their complementary sequence in the target PCR product and thus only detect this specific product. Commonly used probe formats are hydrolysis probes, hybridization probes (e.g., HybProbe probes) or single-labeled probes (e.g., SimpleProbe probes). The probes are coupled to fluorophores that can be measured by the real-time PCR instrument. Several other detection formats are available as well, but are less frequently used. The unique LightCycler HybProbe format is based on the principle of fluorescence resonance energy transfer (FRET).
FRET Fluorescence Resonance Energy Transfer involves transfer of energy from a donor to an acceptor fluorophore. If the donor and the acceptor are in very close proximity, excitation of the donor by blue light results in energy transfer to the acceptor, which can emit light of a longer wave-length. Excitation spectrum of the acceptor must overlap fluorescence emission spectrum of the donor (see figure below).
HybProbe Format
The HybProbe format is suitable for both quantitative PCR and mutation (SNP) detection assays. It uses two specially designed oligonucleotides that hybridize, side by side, to an internal sequence of an amplified fragment during the annealing phase of PCR.
The donor-dye probe is labeled with fluorescein at the 3 end and the acceptordye probe is labeled with LightCycler Red at the 5 end. Hybridization does not take place during the denaturation phase of PCR and, thus, the distance between the dyes is too large to allow energy transfer to occur.
During the annealing phase, the probes hybridize to the amplified DNA fragment in a close head-to-tail arrangement. When fluorescein is excited by the light from the LED, it emits green fluorescent light, transferring the energy to LightCycler Red, which then emits red fluorescent light. This red fluorescence is measured at the end of each annealing step, when the fluorescence intensity is highest. After annealing, the temperature is raised and the HybProbe probe is displaced during elongation. At the end of this step, the PCR product is double-stranded and the displaced HybProbe probes are again too far apart to allow FRET to occur.
Working with DNA
50
1.8.

Sequence-Specific Probe Binding Assays (continued)
One of the advantages of the detection format is that the probes are not altered during PCR. At the end of amplification, both probes are still intact and may be used in a subsequent melting curve experiment (e.g., for mutation detection or SNP analysis). For the design of primers and hybridization probes for use with the LightCycler System Roche Applied Science offers the LightCycler Probe Design Software. For more details please refer to www.lightcycler.com
SimpleProbe Format
SimpleProbe probes are a special type of hybridization probes. They differ from HybProbe probes in one important way: instead of two probes working together, only a single probe is needed. This single probe hybridizes specifically to a target sequence that contains the SNP of interest. Once hybridized, the SimpleProbe probe emits a greater fluorescent signal than it does when it is not hybridized to its target. As a result, changes in fluorescent signal depend solely on the hybridization status of the probe.
During the denaturation phase no hybridization takes place, thus, only a low fluorescence background is detected at 530 nm.
A
During the annealing phase, the probe hybridizes to the amplified DNA fragment and is no longer quenched. Fluorescein, when excited by the LightCycler LED, emits green fluorescent light which is measured only at the end of each annealing step at maximum intensity.
During the subsequent elongation step, the SimpleProbe probe is displaced.
At the end of the elongation step, the PCR product is double stranded and the displaced SimpleProbe probe is again quenched.
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1.8.

Hydrolysis Probe Format
Hydrolysis probe assays, conventionally called "TaqMan"assays, can technically be described as homogenous 5nuclease assays, since a single 3 non-extendable Hydrolysis probe, which is cleaved during PCR amplification, is used to detect the accumulation of a specific target DNA sequence. This single probe contains two labels, a fluorescence reporter and a fluorescence quencher, in close proximity to each other. When the probe is intact, the quencher dye is close enough to the reporter dye to suppress the reporter fluorescent signal (fluorescence quenching takes place via FRET). During PCR, the 5nuclease activity of the polymerase cleaves the Hydrolysis probe, separating the reporter and quencher. In the cleaved probe, the reporter is no longer quenched and can emit a fluorescence signal when excited.
The probe carries two fluorescent dyes in close proximity, with the quencher dye suppressing the reporter fluorescence signal. The 3' end of the Hydrolysis probe is dephosphorylated, so it cannot be extended during PCR. During denaturation the target double-stranded DNA is separated.
A
In the annealing phase of PCR, primers and probes specifically anneal to the target sequence.
As the DNA polymerase extends the primer, it encounters the probe. The polymerase then cleaves the probe with its inherent 5 nuclease activity, displaces the probe fragments from the target, and continues to polymerize the new amplicon.
In the cleaved probe, the reporter dye is no longer quenched and therefore can emit fluorescent light that can be measured by one channel of the LightCycler optical unit, Thus, the increase in fluorescence from the reporter dye directly correlates to the accumulation of PCR products.
Unlike HybProbe probes, hydrolysis probes are digested during PCR. Thus, these probes cannot be used in a subsequent melting curve experiment. This type of assay requires a different experimental approach for detecting a mutation or SNP.
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1.8.

Universal ProbeLibrary
A sophisticated application of the hydrolysis probe format is the Universal ProbeLibrary from Roche Applied Science. The Universal ProbeLibrary contains 165 prevalidated, double-labeled, real-time PCR probes that can be used to quantify virtually any transcript in the transcriptomes of humans, mice, rats, primates, Drosophila, C. elegans, and Arabidopsis. Each of the organism-specific Universal ProbeLibrary Sets can detect 9599% of all transcripts from that organism. This almost universal coverage is due to the length (only 8-9 nucleotides) of the Universal ProbeLibrary probes. Each probe is much shorter than classic, 25- to 35-nucleotide hydrolysis probes. To maintain the specificity, Tm and assay compatibility that hybridization probes require, the duplex-stabilizing DNA analogue LNA (Locked Nucleic Acid) is included in the sequence of each probe. Because it is short, each Universal ProbeLibrary probe can bind to around 7,000 transcripts, while each transcript is detected by around 16 different probes. Yet, only one transcript is detected in a given PCR assay, a specificity ensured by the set of PCR primers chosen. Selection of the correct Universal ProbeLibrary probe and specific PCR primers for a given real-time PCR assay is a simple two-step procedure that involves the ProbeFinder Software, which is available online at the Assay Design Center (http://www.universalprobelibrary.com).
Universal ProbeLibrary assays are compatible with all instruments capable of detecting fluorescein, FITC, FAM and/or SYBR Green I. Universal ProbeLibrary assays have been used successfully on the LightCycler Carousel-Based System, the LightCycler 480 System and other real-time PCR instruments from several suppliers. The powerful combination of the ProbeFinder Software, the Universal ProbeLibrary, and the Transcriptor First Strand cDNA Synthesis Kit, can revolutionize the way you design and perform real-time qPCR assays. For instruments requiring normalization with Rox reference dye choose in addition the new FastStart Universal Probe Master (Rox) from Roche Applied Science. For two-step real-time RT-PCR using the LightCycler Instruments choose the LightCycler 480 Probes Master. For One-Step RT-PCR, the Universal ProbeLibrary probes can be ideally combined on the LightCycler 480 System Master Hydrolysis probes (Cat.No, 04 991 885 001).
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1.8.Quantitative Real-Time PCR

Other Assay Formats Molecular beacons
Hairpin-shaped oligonucleotides oligos with an internally quenched fluorophore whose fluorescence is restored when they bind to a target nucleic acid. The loop portion is complementary to the middle of the expected amplicon and the stem is formed at the annealing temperature of the PCR. For more details refer to http://www.molecularbeacons.com Technology based on a stemloop primer with an integral tail which is used to probe an extension product of the primer thus containing a fluorophore and a quencher. The stemloop tail is separated from the PCR primer by a stopper which prevents stemloop sequences to be copied during PCR. During the annealing step the Scorpion tail curls back to hybridize to the target sequence in the PCR product. As the tail of the scorpion and the PCR product are now part of the same strand of DNA, a fluorescence signal is generated.
Scorpions
Notes
Working with DNA
54
1.8.

Principles of Quantification
Quantification analysis in real-time PCR can be subdivided into two basic types, absolute and relative quantification. Each type uses the experimentally determined CP values differently.
Absolute quantification
In absolute quantification assays, the concentration of the target molecule is expressed as an absolute value (e.g., copies, g/l, etc.). Absolute quantification methods use a standard curve, calculated from external standard samples of known concentration, to determine the concentration of the target molecule in the unknown. Thus, an absolute quantification assay system produces valid results only if the standards and the unknowns are amplified and detected with the same efficiency. Application: Absolute Quantification is very suitable for applications in virology and microbiology where you need to determine the copy number of a specific target, or for the determination of absolute gene copy numbers. In a dual-color set-up, absolute quantification can be combined with internal standards to detect any false negative results. In relative quantification assays, the target concentration is expressed as a ratio of target-to-reference gene in the same sample, rather than an absolute value. The reference gene is an unregulated nucleic acid that is found at constant copy number in all samples.
Relative quantification
Relative quantification methods correct the sample for differences in quality and quantity like variations in initial sample amount, cDNA synthesis efficiency, or sample loading/pipetting errors. Because the quantity of a target and a reference gene is a function only of the PCR efficiency and the sample crossing point, these assays do not require a standard curve in each analysis run. Application: Quantification of mRNA expression levels or determination of gene dosis values. Relative Quantification software, which enables performance of calibrator-normalized relative quantification with PCR efficiency correction, is available for all real-time PCR systems from Roche Applied Science.
For more detailed and up-to-date descriptions of quantitative real-time PCR methods, visit www.lightcycler.com.
Working with DNA
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1.8.

Principles of Quantification (continued)
Absolute Quantification
Relative Quantification
External Standards (mono color detection)
External Standards with internal control (dual color detection)
External Standards without a calibrator
Calibrator normalized relative quantification
Without efficiency correction
With efficiency correction
Notes
Working with DNA
56
1.8.

Melting Curve Analysis
Besides monitoring the PCR process online, real-time PCR instruments (including the LightCycler Carousel-Based System and LightCycler 480 System) can monitor fluorescence changes during temperature transitions. This allows the annealing and denaturation of nucleic acids to be followed in real-time. This procedure, called melting curve analysis, uses either dsDNA-specific dyes (e.g., SYBR Green I) or sequence-specific oligonucleotide probes (e.g., HybProbe or SimpleProbe probes), and can be added at the end of PCR.
Melting Curve Analysis with SYBR Green I
Melting curve analysis with SYBR Green I is used for product characterization, i.e. to determine whether the desired PCR product is free of nonspecific by-products. PCR products can be characterized by melting curve analysis because each double-stranded DNA molecule has a characteristic melting temperature (Tm), at which 50% of the DNA is double-stranded and 50% is melted, i.e. single-stranded. During a melting curve run, the reaction mixture is slowly heated to 95C, which causes dsDNA to melt. A sharp decrease in SYBR Green I fluorescence occurs when the temperature reaches the Tm of a PCR product present in the reaction. For instruments requiring normalization with Rox reference dye choose the new FastStart Universal SYBR Green Master (Rox) from Roche Applied Science.
Genotyping with HybProbe and SimpleProbe Probes and SNP Detection
In a genotyping experiment with HybProbe probes, one HybProbe oligonucleotide hybridizes to a part of the target sequence that is not mutated; this probe functions as an anchor. The other HybProbe oligonucleotide (mutation or detection probe) spans the mutation site and has a Tm approx. 5C lower than the Tm of the anchor probe. As the temperature increases, the shorter mutation probe dissociates first. When this happens, the two dyes are no longer close and the fluorescence signal decreases. Because the Tm of a probe-target hybrid depends not only on the length and the GC content of the probe, but also on the degree of homology in the hybrid, perfectly bound probes separate at a higher Tm than those that are bound to DNA containing a destabilizing mismatch.
The precise temperature control of the LightCycler Carousel-Based System and LightCycler 480 System allow these instruments to monitor specific fluorescent-labeled probes as they melt off a target sequence. When melting curve analysis is used to monitor the melting of short duplexes, such as hybrids between HybProbe or SimpleProbe probes and target, the assay can identify even single base alterations in the amplicon. Thus, this is an ideal tool for detection of Single Nucleotide Polymorphisms (SNPs) or genotyping.
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1.8.

Melting Curve Analysis (continued)
High resolution melting curve analysis
A new class of non-sequence specific DNA dyes (e.g., LightCycler 480 ResoLight dye)bind to double-stranded DNA Sequence in a saturating manner and therefore give very uniform, sharp signals during melting curve analysis. These binding characteristics can be used to detect subtle differences in sequence between samples (e.g., SNPs, mutations), or within a sample (e.g., to differentiate heteroduplex from homoduplex DNA to identify heterozygotes). Due to its uniform thermal profile across a plate and its optical system, the LightCycler 480 System enables the acquisition and analysis of melting curves at high resolution. The LightCycler 480 High Resolution Melting Master is available to support this method. Sequence variants resulting in different melting curve shapes can be detected using LightCycler 480 Gene Scanning Software (Cat. No. 05 103 908 001). An overview of melting curve-based methods supported on the LightCycler 480 System is shown in the figure below.
SYBR Green I for Product Identification
High Resolution Melting Dye for Gene Scanning
Fluorescence labeled Probes for Genotyping
For up-to-date information on genotyping methods, visit www.lightcycler480.com.
Working with DNA
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1.9.
1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15.
References
Ausubel, F. M. et al., (1991) In: Current Protocols in Molecular Biology. John Wiley and Sons, New York Brown, T. A. (1991) In: Molecular Biology LabFax. Bios Scientific Publishers, Academic Press Nonradioactive In Situ Hybridisation Application Manual (2002) Roche Applied Science Nucleic Acid Isolation and Purification Manual (2002) Roche Applied Science Roche Applied Science, Technical Data Sheets PCR Application Manual (2006) Roche Applied Science PCR Grade Deoxynucleotides (2001) Roche Applied Science Rolfs, A. et al., (1992) PCR Clinical Diagnostics and Research. New York: Springer Verlag Sambrook. J., Fritsch, E. J. and Maniatis, T. (1989) In: Molecular Cloning, A Laboratory Manual, 2nd edition. Cold Spring Harbor Laboratory Press The DIG Application Manual for Filter Hybridisation (2001) Roche Applied Science Molecular Weight Markers for Nucleic Acids (2000) Roche Applied Science Nasri, M. et al., (1986) Nucleic Acid Research 14, 811 Frey, B. et al., (1995) Biochemica 2, 8 9 DIG Product Selection Guide (2007) Roche Applied Science LightCycler System (2004) Roche Applied Science
Working with RNA

Chapter 2
2.1. 2.2. 2.3. 2.4. 2.5. 2.6. 2.7.
Precautions for handling RNA ....................................... Commonly used formulas ................................................ Isolating and purifying RNA ........................................... Analyzing RNA .................................................................... RT-PCR ................................................................................... Labeling of RNA .................................................................. References ............................................................................
60 63 65 68 70 79 81
2.1.
Precautions for handling RNA

Working with RNA is more demanding than working with DNA, because of the chemical instability of the RNA and the ubiquitous presence of RNases. Unlike DNases, RNases do not need metal ion co-factors and can maintain activity even after prolonged boiling or autoclaving. Therefore special precautions should be taken when working with RNA. Always wear gloves when working with RNA. After putting on gloves, dont touch surfaces and equipment to avoid reintroduction of RNases to decontaminated material. Designate a special area for RNA work only. Treat surfaces of benches and glassware with commercially available RNase inactivating agents. Clean benches with 100% ethanol. Use sterile, disposable plasticware. Electrophoresis tanks for RNA analysis can be cleaned with 1% SDS, rinsed with H2O, then rinsed with absolute ethanol and finally soaked in 3% H2O2 for 10 min. Rinse tanks with DEPC-treated H2O before use.
General Information
Gloves and contact
Workspace and working surfaces Equipment and disposable items
Glass and plasticware
Glassware should be baked at 180 200C for at least 4 hours. Autoclaving glassware is not sufficient to eliminate RNases. Use commercially available RNase free plasticware. If plasticware should be reused, soak (2 h, 37C) in 0.1 M NaOH/1 mM EDTA (or absolute ethanol with 1% SDS), rinsed with DEPC treated H2O and heated to 100C for 15 min. Corex tubes should be treated with DEPC treated H2O overnight at room temperature, then autoclave for 30 min. to destroy unreacted DEPC. Incubate for 30 s in 70% ethanol, 5 min in 1 M NaOH, and rinse with DEPC-treated H2O.
Cleaning of pH electrodes
DEPC = diethylpyrocarbonate
Working with RNA
60
2.1.

Purchase reagents that are free of RNases. Reserve separate reagents for RNA work only: Wear gloves, use baked spatulas and untouched weigh boats or weigh paper. All solutions should be made with DEPC-treated H2O (see page 155). Extract RNA as quickly as possible after obtaining samples. For best results, use either fresh samples or samples that have been quickly frozen in liquid nitrogen and stored at 70C. This procedure minimizes degradation of crude RNA by limiting the activity of endogenous RNases. Blood and bone marrow samples can be stabilized with commercial available stabilization reagentsa. All required reagents should be kept on ice.
Reagents
Handling fresh and stored material before extraction of RNA
e.g., RNA/DNA Stabilization Reagent for Blood and Bone Marrow (Cat. No. 11 934 317 001), available from Roche Applied Science
RNase inhibitors
RNase inhibitors* can be used to protect RNA from degradation during isolation and purification and in all downstream applications. The most commonly used inhibitor is a eukaryotic protein that inactivates RNases, via a non-covalent and reversible binding. Use an RNase Inhibitor that is active during cDNA synthesis and can protect RNA, like Protector RNase Inhibitor which is active up to 60C. To keep the inhibitor active, avoid solutions with strong denaturing agents such as SDS or urea, maintain reducing conditions (1 mM DTT) and hold the temperature below 65C. Other inhibitors include macaloid and vanadyl-ribonucleoside complexes. Store RNA, aliquoted in ethanol or isopropanol at 70C. Most RNA is relatively stable at this temperature. Remove ethanol or isopropanol by centrifugation and resuspend in the appropriate RNase-free buffer. Store cDNA if possible. Always keep the RNA sample on ice when preparing an experiment. Avoid overdrying of RNA after ethanol precipitation. Dry in vacuum or for 15 min at room temperature in a clean space.
Storage of RNA
Manipulation of RNA Drying RNA
* Product available from Roche Applied Science: Protector RNase Inhibitor (Cat. No. 03 335 399 001 2000 U; Cat. No. 03 335 402 001 10000 U)
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61
2.1.

Dissolve RNA by adding RNase-free buffer or H2O and incubate the tube on ice for 15 minutes. Gently tap the tube or vortex with care. Use RNase-free tips or autoclave regular tips. Keep pipettes clean. RNA is not stable at elevated temperatures, therefore, avoid high temperatures (> 65C) since this will affect the integrity of the RNA. To melt secondary structures, heat RNA to 65C for 15 min. in the presence of denaturing buffers.
Dissolving RNA Pipetting RNA Temperature sensitivity
Notes
Working with RNA
62
2.2.

Average molecular weight (MW) of a ribonucleotide: 340 Dalton (Da)
MW of ssRNA = [number of bases] x [340 Da]
Calculation of Molecular Weights in Dalton Conversion of g to pmol
e.g., MW of tRNA from E. coli (75 bases) = 25.5 x 103 Da = 25.5 kDa
106 pg 1 pmol 1 g (of ssRNA) x 2,941 x x = 1 g 340 pg Nb Nb 1 x 2,941 = 29.4 pmol 100
pmol of ssRNA = g (of ssRNA) x
e.g., 1 g of a 100 base ssRNA molecule =
The value calculated with this formula also represents the pmoles of 5 or 3 ends.
Calculation of pmol of 5 (or 3) ends
Nb = number of bases
see above calculation of conversion of g to pmol
Conversion of pmol to g
g of ssRNA = pmol (of ssRNA) x
340 pg 1 g x x Nb 1 pmol 106 pg
= pmol (of ssRNA) x Nb x 3.4 x 10-4 e.g., 1 pmol of a 250 base ssRNA molecule = 0.085 g
Nb = number of bases
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2.2.

Examples
Type tRNA 5S rRNA 16S rRNA 23S rRNA 18S rRNA 28S rRNA 18S rRNA 28S rRNA 18S rRNA 28S rRNA 18S rRNA 28S rRNA Length (in bases) 75 120 1 541 2 904 1 976 3 898 1 869 4 712 1 868 5 025 2 366 6 333 MW (in kDa) 26 41 523 987 672 1.3 x 103 635 1.6 x 103 635 1.7 x 103 804 2.15 x 103
Organism E. coli, gram negative bacterium
Drosophila melanogaster, fruitfly Mus musculus, mouse
Homo sapiens, human
Oryctolagus cuniculus, rabbit
Notes
Working with RNA
64
2.3.
Isolating and purifying RNA

Origin Cultured cells, tissues, total RNA Recommendation* mRNA Isolation Kit mRNA Capture Kit Human whole blood/bone marrow Cultured cells, bacteria, yeast, blood Tissue mRNA Isolation Kit for Blood/Bone marrow High Pure RNA Isolation Kit High Pure RNA Tissue Kit TriPure Isolation Reagent High Pure RNA Paraffin Kit
Use this chart to select a product according to the type and origin of RNA (see also reference 3).
Type
mRNA
total RNA
Cultured cells, tissues, bacteria, yeast, blood Formalin-fixed, paraffin-embedded tissue, fresh-frozen tissue samples Formalin-fixed, paraffin-embedded tissue
High Pure FFPE RNA Micro Kit High Pure Viral RNA Kit Quick Spin Columns
Viral RNA RNA fragments
Serum, plasma, other body fluids, cell culture supernatant Removal of unincorporated nucleotides from labeled RNA molecules
Mini Quick Spin Columns * The amount of RNA that can be isolated with the kits depends on a variety of variables like the amount of sample applied, concentration of RNA within the sample, buffer systems, etc. Please refer to page 66 for a detailed overview.
Use this chart to select a product according to the main application in which the RNA will be used (see reference 3).
Product High Pure RNA Tissue Kit High Pure RNA Paraffin Kit High Pure FFPE RNA Micro Kit High Pure RNA Isolation Kit High Pure Viral RNA Kit mRNA Isolation Kit for Blood/Bone Marrow mRNA Isolation Kit mRNA Capture Kit TriPure Isolation Reagent mini Quick Spin RNA Columns Quick Spin Columns * DD = differential display RT-PCR DD*-RT-PCR cDNA Synthesis Northern Blotting RNase protection In Vitro Translation
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65
2.3.

Quantity of starting material Tissue: 1 10 mg Blood: 200 500 l Cultured cells: 10 6 cells Yeast: 10 8 cells Bacteria: 10 9 cells 200 600 l of serum, plasma, urine, cell culture supernatant up to 20 m FFPE fresh-frozen tissue section Typical Yield 0.5 3.0 g/mga for 10 RT-PCR Reactions 20 gb 20 g 35 50 g Product detectable by RT-PCR
Use this chart to select a product according to its characteristics (see also reference 3).
Product High Pure RNA Tissue Kit High Pure RNA Isolation Kit
High Pure Viral RNA Kit
High Pure RNA Paraffin Kit
0.3 to 1.5 g/5 m section 2 6 g/20 mg tissue 1.5 3.5 g/5 m
High Pure FFPE RNA Micro Kit

a depends b
1 10 m FFPE tissue sections
on type of tissue depends on type of cells
Use this chart to select a product according to its characteristics (see also reference 3).
Product mRNA Isolation Kit Quantity of starting material Tissue: 50 mg 1 g Cells: 2 x 105 10 8 total RNA: 250 g 2.5 mg Tissue: up to 20 mg Cells: up to 5 x 105 total RNA: up to 40 g RNA from liver, spleen: 50 mg 1 g Cultured epithelial cells, fibroblasts: 10 6 107 20 75 l labeling mixture Yield 7 14 g/100 mg tissuea 0.3 25 g/107 cellsb 1 5 g/100 g total RNA Product detectable by RT-PCR
mRNA Capture Kit
TriPure Isolation Reagent
6 10 g/mg tissuea 8 15 g/10 6 cellsb > 80% Exclusion limit: > 80%
mini Quick Spin RNA Columns
20 bp
Quick Spin Columns

a b
50 l labeling mixture
depends on type of tissue depends on type of cells
Note: For more information on nucleic acid isolation and purification please visit http://www.roche-applied-science.com/napure
Working with RNA
66
2.3.
107 cells

RNA content in various cells and tissues (see also reference 3)
3T3 ~120 ~3 Hela ~150 ~3 COS ~350 ~5
total RNA (g) mRNA (g)
mouse tissue (100 mg) total RNA (g) mRNA (g)
Brain ~120 ~5
Heart ~120 ~6
Intestine ~150 ~2
Kidney ~350 ~9
Liver ~400 ~14
Lung ~130 ~6
Spleen ~350 ~7
Notes
Working with RNA
67
2.4.
Analyzing RNA
Concentration via OD Measurement
Concentration of RNA Notes
1 A260 Unit of ssRNA = 40 g/ml H2O OD value should range between 0.1 and 1.0 to ensure an optimal measurement. The above mentioned value is based on the extinction coefficient of RNA in H2O. Please note that this coefficient and hence the above mentioned value may differ in other buffers and/or solutions. Cuvettes should be RNase free (see chapter 2.1. Precautions for handling RNA, page 60) Example of calculation: volume of ssRNA sample: 100 l dilution: 25 l of this sample + 475 l H2O (1/20 dilution) A260 of this dilution: 0.56 concentration of ssRNA in sample: 0.56 x 40 g/ml x 20 (= dilution factor) = 448 g/ml amount of ssRNA in sample: 448 g/ml x 0.1 ml (= sample volume) = 44.8 g
Purity via OD Measurement Purity of RNA Notes
Pure RNA: A260/A280
2.0
Buffered solutions provide more accurate values than water since the A260/A280 ratio is influenced by pH. Therefore, it is recommended to measure the ratio in a low salt buffer. Pure RNA has a ratio of 1.9 2.1 in a 10 mM Tris buffer. An A260/A280 smaller than 2.0 means that the preparation is contaminated with proteins and aromatic substances (e.g., phenol). In this case, it is recommended to purify the RNA (again) before using it in subsequent applications. The OD value gives no indication about the size of the RNA.
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2.4.
Analyzing RNA
Size estimation of RNA fragments
Agarose Electrophoresis
In most cases, 1% Agarose MP** gels (or variations between 0.8 and 1.2%) are used to separate ssRNA molecules. Denaturing conditions*** are crucial for the resolution and visualization of the different fragments in a given gel. Efficient range of separation of ssRNA molecules: 3.5% of Acrylamide/Bisacrylamide (29/1): 750 2,000 5.0% of Acrylamide/Bisacrylamide (29/1): 200 1,000 8.0% of Acrylamide/Bisacrylamide (29/1): 50 400 A variety of different molecular weight markers are available from different suppliers. Roche Applied Science offers: RNA Molecular Weight Marker I, DIG-labeled (0.3 6.9 kb), Cat. No. 11 526 529 910 9 fragments: 310, 438, 575, 1049, 1517, 1821, 2661, 4742, 6948 bases RNA Molecular Weight Marker II, DIG-labeled (1.5 6.9 kb), Cat. No. 11 526 537 910 5 fragments: 1517, 1821, 2661, 4742, 6948 bases
Acrylamide Electrophoresis
Size Markers
(0.3 1.5 kb), Cat. No. 11 373 099 910 5 fragments: 310, 438, 575, 1049, 1517 bases (For more information please refer to reference 10) Bacterial 23S* (~ 2,900 b) and/or 16S* (~1,550 b) ribosomal RNAs can also be used as size markers.
* Products available from Roche Applied Sience ** Agarose Multi Purpose available from Roche Applied Science (Cat. No. 11 388 983 001 100 g; Cat. No. 11 388 991 001 500 g) is a high gel strength agarose (> 1,800 g/cm2: 1%) permitting the use of very low and very high concentrations, resulting in a broad range of linear RNA molecules that can be separated in the same type of agarose. This agarose is also function tested for the absence of DNases and RNases. *** Please refer to chapter 5 Preparing Buffers and Media for recipes to prepare the necessary buffers.
RNA Molecular Weight Marker III, DIG-labeled
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2.5.
RT-PCR
Reaction Components: Template
Avoiding contamination Type
Please refer to chapter 1.7. Amplification of DNA: Avoiding contamination (page 36) for the different sources of possible contaminations before and during amplification reactions and how to most optimally avoid them. If possible, use purified mRNA as a template rather than total RNA. Starting with poly (A+) mRNA will improve the likelihood of successful amplification of rare mRNAs since the proportion of mRNAs in a total RNA preparation is very low (typically 1 5% of total RNA for a mammalian cell). If a mRNA template is used and enough material is available, the integrity of the mRNA can be checked by gel electrophoresis before using it in a RT-PCR. The mRNA should appear as a smear between 500 bp and 8 kb. Most of the mRNA should be between 1.5 and 2 kb. To minimize the activity of RNases that are released during cell lysis, include RNase inhibitors* in the lysis mix or use methods (ref. 6 and 7) that simultaneously disrupt cells and inactivate RNases.
Integrity
Avoiding RNase contamination
Please refer to chapter 2.1. Precautions for handling RNA (pages 60 62) for a comprehensive overview how to avoid RNase contamination. The most commonly used inhibitor is a eukaryotic protein that inactivates RNases, via a non-covalent and reversible binding.
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2.5.
RT-PCR
Reaction Components: Choice of reverse transcription primers
The primer used for reverse transcription affects both the size and the specificity of the cDNA produced. Four kinds of primers are commonly used in RT-PCR and each has its advantages:
Oligo(dT)N
Generates full-length cDNAs. If template contains oligo(A) stretches, the primer may bind these and lead to mispriming. Prevents priming from internal sites of the poly(A) tail. Generates full-length cDNA. Preferred priming method for most two-step RT-PCR applications. Available as part of the Transcriptor First Strand cDNA Synthesis Kit.* Provides uniform representation of all RNA sequences in mRNA. Can prime cDNA transcription from RNAs that don't contain a poly(A) tail. Adjusting the ratio of random primers to RNA in the RT reaction controls the average length of cDNAs formed. Example: A high ratio will generate relatively short cDNAs, which will increase the chances of copying the complete target sequence. Short cDNA transcripts may be ideal way to overcome difficulties presented by RNA secondary structures.
Anchored oligo(dT)N
Random hexamers*
Sequence-specific
Selects for a particular RNA, e.g., for diagnostic purposes. Greatly increases the specificity of the RT-PCR. Only type of priming that can be used for one-step applications.
* Product available from Roche Applied Science: Transcriptor First Strand cDNA Synthesis Kit, Cat. No: 04 379 012 001 1 kit (50 rxns, including 10 control rxns); 04 896 866 001 1 kit (100 rxns); 04 897 030 001 1 kit (200 rxns); Primer random, Cat. No: 11 034 731 001.
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2.5.
RT-PCR
Reaction Components: Design of reverse transcription primers
RT-PCR amplification of a particular mRNA sequence requires two PCR primers that are specific for that mRNA sequence. The primer design should also allow differentiation between the amplified product of cDNA and an amplified product derived from contaminating genomic DNA. There are two different strategies to design the required primersa:
Strategy 1
See panel 1 on next page: Design primers that anneal to sequences in exons on both sides of an intron. With these primers, any product amplified from genomic DNA will be much larger than a product amplified from intronless mRNA. See panel 2 on next page: Design primers that span exon/exon boundaries on the mRNA. Such primers should not amplify genomic DNA.
Strategy 2
Please also refer to reference 4.
Working with RNA
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2.5.
RT-PCR
Reaction Components: Template Design Start with the purest RNA template possible
Purity of template
If your target is mRNA, start with purified mRNA as template, rather than total RNA. (The proportion of mRNA in a total RNA preparation is quite low.) This will greatly increase the likelihood of successfully amplifying rare mRNAs. Use a template preparation product that is specifically designed for RNA purification. For details on RNA purification products available from Roche Applied Sciences, see page 65. If your target is mRNA, check the integrity of the mRNA by gel electrophoresis. The mRNA should appear as a smear between 500 bp and 8 kb. Most of the mRNA should be between 1.5 kb and 2 kb. If your target is eukaryotic total RNA, check the integrity of the total RNA by gel electrophoresis. The total RNA is dominated by ribosomal RNA, so the 18S and 28S rRNA should be appear as clear bands.
Quality of template
Eliminate RT inhibitors from the template preparation.
Before using it as a template, precipitate the RNA using ethanol, then wash it once with 70% ethanol. Be sure to remove all traces of ethanol before using the RNA in the RT reaction. Use a product specifically designed for RNA purification to prepare the template. Such products can help eliminate potential inhibitors during purification. For details on RNA purification products available from Roche Applied Sciences, see page 65.
Intactness of template Take rigorous and repeated precautions to prevent RNase contamination
during cell lysis during the purification procedure
Use isolation methods that simultaneously disrupt cells and inactivate RNases (by adding SDS or guanidine). Even if you don't think RNases could be present at a particular step, act as though they are present. Include RNase inhibitors (e.g., Protector RNase Inhibitor*) in non-denaturing purification steps. Use only sterile, RNase- and DNase-free plastic disposables (pipette tips, etc.).
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2.5.
RT-PCR
Reaction Components: Template Design
Sterilize all glassware before use. (RNases can be present on non-sterile glassware.). Always wear gloves throughout the isolation process. (Skin is a rich source of RNases.). If necessary, analyze the product of each step in the isolation process by gel electrophoresis to ensure that the RNA is still RNase-free. after purification Short-term storage: Store the purified RNA template at +2 to +8C until use. Long-term storage: Store the purified RNA template at -70C. If possible, store cDNA, it is more stable than RNA.
Notes
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2.5.
RT-PCR
Reaction Components: Choice of enzymes
Temperature optima
Higher incubation temperatures help eliminate problems of template secondary structures. High temperature improves the specificity of reverse transcription by decreasing false priming. Thermoactive reverse trancriptases that can be incubated at higher temperatures (50 70C) are more likely to produce accurate copies of mRNA, especially if the template has a high GC content. Transcribe GC-rich templates with high secondary structures at 55C 65C with the thermostable Transcriptor Reverse Transcriptase* or Transcriptor First Strand cDNA Synthesis Kit* Most reverse transcriptases require divalent ions for activity. Enzymes that use Mg2+ are likely to produce more accurate cDNA copies than those that use Mn2+ since Mn2+ adversely affects the fidelity of the DNA synthesis. Reverse transcriptases have different ability to copy smaller amounts of template (see product characteristics table in this chapter, page 78).
Divalent ion requirement
Sensitivity
* Product available from Roche Applied Science: Transcriptor Reverse Transcriptase (Cat. No: 03 531 317 001 250 U, 03 531 295 001 500 U, 03 531 287 001 2,000 U); Transcriptor First Strand cDNA Synthesis Kit (Cat. No: 04 379 012 001 1 kit (50 rxns, including 10 control rxns); 04 896 866 001 1 kit (100 rxns); 04 897 030 001 1 kit (200 rxns)).
Specificity
Reverse transcriptases differ in their ability to transcribe RNA secondary structures accurately (see product characteristics table in this chapter, page 78). Using different reverse transcriptase DNA polymerase combinations will allow to optimally amplify certain target length.
Reverse Transcriptase DNA polymerase combinations
Working with RNA
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2.5.
RT-PCR
Procedures
One tube One Step procedure Both cDNA synthesis and PCR amplification are performed with the same buffer and site-specific primers, eliminating the need to open the reaction tube between the RT and PCR steps
Two Step procedure Two tube, two step procedure: In the first tube, the first strand cDNA synthesis is performed under optimal conditions. An aliquot of this RT reaction is then transferred to another tube containing all reagents for the subsequent PCR. One tube, two step procedure: In the first step, the reverse transcriptase produces firststrand cDNA synthesis in the presence of Mg2+ ions, high concentrations of dNTPs and primers. Following this reaction, PCR buffer (without Mg2+ ions), a thermostable DNA Polymerase and specific primers are added to the tube and the PCR is performed.
Advantages of Two Step procedure Optimal reaction conditions:

The two step format allows both reverse transcription and
Advantages of One tube One Step procedure Minimal time required: The one step reaction has fewer pipetting steps than the two step reaction, thereby significantly reducing the time needed for the experiment and eliminating pipetting errors. Reduced risks for contamination: The entire one step reaction takes place in a single tube with no transfers required and no need to open the reaction tube. (steps where contamination can occur). Improved sensitivity and specificity: Two characteristics of the one step reaction provide increased yield and efficiency: the cDNA reaction is performed at a high temperature thereby eliminating problems with secondary RNA structures. the entire cDNA sample is used as template for the PCR. Use of sequence-specific primers enhance specificity and sensitivity.
PCR to be performed under optimal conditions ensuring an efficient and accurate amplification. Flexibility: Two step procedures allow the product of a single cDNA synthesis reaction to be used in several PCR reactions for analysis of multiple transcripts. Allows choice of primers (oligo (dT), anchored oligo (dT), random hexamer or sequence-specific primers). Allows a wider choice of RT and PCR enzymes. Amplifies long sequences:
With the right combination of reverse transcriptases and
thermostable DNA polymerases, two step RT-PCR can amplify RNA sequences up to 14 kb long.
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2.5.
RT-PCR
Reaction Components: Choice of enzyme for One-Step and Two-Step PCR
Two-Step RT-PCR
Product Size
12 kb 9 kb 6 kb 3 kb
One-Step RT-PCR
Yield Sensitivity Difcult Templates Reaction Temperature Full-Length cDNA
42 65C
Transcriptor Reverse Transcriptase
42 65C
Transcriptor First Strand cDNA Synthesis Kit
40 60C
Titan One Tube RT-PCR System / Kit
60 70C
C. therm One Step RT-PCR System
Reaction Components: Choice of enzyme for Two-Step RT-PCR.

Transcriptor Reverse Transcriptase Enzyme component Product size Priming Reaction temperature RNase H activity Sensitivity A new recombinant Reverse Transcriptase Up to 14 kb Oligo d(T), Specific, random hexamers 42C - 65C Yes ++++
Ability to transcribe difficult templates ++++ Full length cDNA Incorporation of modified nucleotides Product configuration ++++ Yes Enzyme Reaction buffer Robust reverse transcription of all kinds of templates Specially usefull for difficult templates Generation of full length cDNAs
Intended use
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77
Reaction Components: Choice of enzyme for One-Step RT-PCR.

Tth DNA Polymerase Enzyme component C. Therm One Step RT-PCR System Titan One Step RT-PCR System Blend of AMV Reverse Transcriptase, Taq DNA Polymerase and a Proofreading Polymerase Up to 6 kb Specific 45C - 60C Yes +++ +
Thermostable DNA polymerase Blend of C. therm and Taq DNA with intrinsic reverse transcripase Polymerase activity Up to 1 kb Specific 55C - 70C No + + Up to 3 kb Specific 60C - 70C No ++ +++
Product size Priming Reaction temperature RNase H activity Sensitivity Ability to transcribe difficult templates Full length cDNA Incorporation of modified nucleotides Carry-over prevention
Yes
+ Yes
++ Yes
++
Tth DNA Polymerase Product configuration Enzyme PCR reaction buffer RT-PCR reaction buffer Mn(OAc)2 solution
C. Therm One Step RT-PCR System Enzyme Blend Reaction Buffer DMSO solution DTT solution
Titan One Step RT-PCR System Enzyme Blend Reaction Buffer MgCl2 solution PCR grade Water DTT solution One-Step RT-PCR for fragments up to 6 kb, with high sensivity Synthesis of full length cDNAs
Intended use
One-Step RT-PCR of short normal templates
One-Step RT-PCR of difficult (e.g. GC-rich) templates
Benefit from the availability of a broad range of reverse transcriptases, to find the best possible product for your application. Get the most out of your precious RNA samples and your assays, by using well characterized reverse transcriptases that are function tested over a broad range of different applications.
Working with RNA
78
2.6.
Labeling of RNA
Overview of different techniques
Labeling Method Labeling RNA by in vitro Transcription 5'End labeling* 3'End labeling* Labeling RNA by in vitro Transcription 5'End labeling* 3'End labeling * Labeling RNA by in vitro Transcription 5'End labeling* 3'End labeling* Relative sensitivity +++ ++ ++ +++ ++ ++ +++ ++ ++
Application Northern Blotting Southern Blotting
Dot/Slot Blotting
In Situ Hybridisation
* Note: Please refer references 8, 9, 11 for an overview and a selection help for DIG labeling of nucleic acids.
Principle of In Vitro Transcription with DNA dependent RNA Polymerases

T7 RNA Polymerase promotor sequence SP6 RNA Polymerase promotor sequence
DNA Template
5'P
GAATTCATGCATG 3'OH 3'OH CTTAAGTACGTAC
5'P
Transcription with T7 Polymerase T7 RNA Polymerase 5'P GAATTCATGCATG 3'OH 3'OH CTTAAGTACGTAC 5'P 5'P
Transcription with SP6 Polymerase SP6 RNA Polymerase CATGCATGAATTC 3'OH 3'OH GTACGTACTTAAG 5'P
Synthesized RNA strand
5'P GAAUUCAUGCAUG 3'OH
Synthesized RNA strand
5'P CAUGCAUGAAUUC 3'OH
Please refer to pages 88 91 for further information on the conversion of nucleic acid to proteins.
Working with RNA
79
2.6.
Labeling of RNA
SP6, T7 and T3 Polymerases
Properties 10 x Transcription buffer Application and typical results
DNA dependent RNA Polymerases, specific for their corresponding promotor. 400 mM Tris (pH 8.0), 60 mM MgCl2, 100 mM DTT, 20 mM spermidine Buffer without nucleotides is stable at 15 to 25C, store in aliquots. Generate homogeneously labeled single stranded RNA molecules as probes for hybridisation experiments. Radioactive nucleotides (32P, 35S) and non-radioactive nucleotides (biotin, digoxigenin, fluorochromes) can be incorporated.
Standard Assay:
Components Template DNA Nucleotides, final concentration Radioactive 0.5 g ATP, GTP, UTP each 0.5 mM final Non-radioactive* 1 g ATP, GTP, CTP, each 1 mM final UTP 0.65 mM final DIG, Biotin or fluorochrome UTP, 0.35 mM final 2 l 40 units 20 units Add H2O to 20 l 2 hours/37C 2 l 40 units 20 units Add H2O to 20 l 2 hours/37C Cold (without label) 1 g ATP, GTP, CTP, UTP each 1 mM final
Labeled nucleotide, [32P] CTP final concentration (400 Ci/mmol), 50 Ci (1.85 MBq/mmol) 10 x transcription buffer RNA Polymerase RNase Inhibitor H2O Incubation 2 l 20 units 20 units Add H2O to 20 l 20 min/37C
This standard assay incorporates > 50% of the input radioactivity

Add 2 l 0.2 M EDTA and/or heat to 65C for 10 min.
* For a complete overview, please refer to references 8 and 9.
Working with RNA
80
2.7.
1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11.
References
Ausubel, F. M. et al., (1991) In: Current Protocols in Molecular Biology. John Wiley and Sons, New York Brown, T. A. (1991) In: Molecular Biology LabFax. Bios Scientific Publishers, Academic Press Nucleic Acid Isolation and Purification Manual (2007), Roche Applied Science PCR Application Manual (2006), Roche Applied Science Roche Applied Science, Technical Data Sheets Rolfs, A. et al., (1992) PCR Clinical Diagnositcs and Research, New York: Springer Verlag Sambrook. J., Fritsch, E. J. and Maniatis, T. (1989) In: Molecular Cloning, A Laboratory Manual, 2nd edition. Cold Spring Harbor Laboratory Press The DIG Application Manual for Filter Hybridisation (2001) Roche Applied Science DIG Product Selection Guide (2007) Roche Applied Science Tools for Mapping and Cloning (2006) Roche Applied Science Nonradioactive In Situ Hybridization Application Manual (2002) Roche Applied Science
Working with Proteins

Chapter 3
3.1. 3.2. 3.3. 3.4. 3.5. 3.6.
Precautions for handling Proteins ................................ 82 Conversion from Nucleic Acids to Proteins .............. 88 Analyzing Proteins .............................................................. 92 Quantification of Proteins ................................................ 98 Purifying Proteins ............................................................ 102 References ......................................................................... 112
3.1.
Precautions for handling Proteins

For successful isolation or purification of proteins from biological extracts, include protease inhibitors throughout the procedure. Proteases are ubiquitous and difficult to separate from proteins. As a general rule: assume that proteases are present, inhibit early and inhibit often (for more detailed information, please refer to page 83 and/or reference 1). The regulation of many biological processes and pathways is accomplished by the formation and cleavage of phosphate esters. The phosphorylation of proteins is carefully balanced by an interplay of protein kinases and phosphatases. Phosphatases are ubiquitous. A preservation of the phosphorylation pattern is important to get an accurate view about the general or specific phosphorylation status (for more detailed information, please refer to page 84). Aliquot protein solutions and store at different temperatures and in different buffer systems. Test activity of the protein to find out the most optimal storage condition. Refrigeration with the appropriate stabilization reagent is often sufficient to maintain the biological activity of proteins.
Avoiding degradation of proteins
Avoiding dephosphorylation of proteins
Storage of proteins
For protein solutions in glycerol (50%, v/v) or suspensions in ammonium sulfate (3.2 M), freezing should be avoided, because of the cold denaturation effect. Ice crystals can cause physical shearing and denaturation of proteins. Avoid repeated freezing and thawing of enzyme solutions. If the enzyme is to be stored frozen, store it in small portions. Shock freezing of proteins in liquid nitrogen and long term storage can be performed after addition of 10 20% glycerol.
Manipulation of proteins
Always keep the protein sample on ice during experiments. Use a fresh pipette tip for each sample that has to be removed from the parent vial. Never return unused material to the parent vial. Always wear gloves to prevent contamination with other proteins and proteases. Avoid vigorous vortexing and pipetting of protein solutions to minimize denaturation. Avoid dust forming during the experiment dust contains approximately 60% ceratines (approx. 60 kD). Always work with small quantities in small volumes to avoid contamination and work as quickly as possible.
82
3.1.

Proteases are ubiquitous in all living cells. At the time of cell lysis, proteases are released and can quickly degrade any proteins in the extract. During isolation and purification, proteolytic damage can affect functionality and reduce yields of protein. To get a complete protection against a multitude of proteases different protease inhibitors are needed. cpmplete Protease Inhibitor Cocktail Tablets* eliminate the time-consuming search for the right protease inhibitors. cpmplete inhibits proteolytic activity in extracts from almost any tissue or cell type, including animals, plants, yeast, bacteria, and fungi (for examples, see www.roche-applied-science.com/proteaseinhibitor). The non-toxic cpmplete tablets inhibit a multitude of protease classes, including serine proteases, cysteine proteases, and metalloproteases. cpmplete as EDTA-free* version maintain the stability of metal-dependent proteins and effectiveness of purification techniques (i.e., IMAC [immobilized metal affinity chromatography] for isolation of Poly-His-tagged proteins)
Inhibition of protease activity
* Product available from Roche Applied Science, cpmplete Cat. No. 04 693 116 001, Pack size 20 tablets (each for 50 ml); cpmplete, EDTA-free Cat. No. 04 693 132 001, Pack size 20 tablets (each for 50 ml). For other pack sizes and more information visit: www.roche-applied-science.com/proteaseinhibitor COMPLETE is a trademark of Roche.
Notes
83
3.1.

The phosphorylation states can be the difference between an active and an inactive protein. To avoid that this states change during protein purification or analysis individual phosphatase inhibitors or a cocktail against a broad range of phophatases can be used. PhosSTpP Phosphatase Inhibitor Cocktail Tablets* eliminate the timeconsuming search for the right phosphatase inhibitors. PhosSTpP protects phosphorylated protein(s) against dephosphorylation. It shows an effective inhibition of a broad spectrum of phosphatases such as acid and alkaline phosphatases, serine/threonine phosphatase classes (e.g., PP1, PP2A and PP2B), tyrosine phosphatase (PTP), and dual-specific phosphatases. The tablets inhibit phosphatases in a variety of sample materials including mammalian, insect, or plant cells. PhosSTpP is also well-suited for buffers containing formalin for the formalin-fixation of paraffin-embedded (FFPE) tissue sections. The non-toxic PhosSTpP tablets are easy-to-use and can be combined with cpmplete Protease Inhibitor Cocktail Tablets to simultaneously protect proteins against dephosphorylation and proteolytic degradation.
Inhibition of phosphatase activity
* Product available from Roche Applied Science, Cat. No. 04906845001 Pack size 10 tablets (each for 10 ml). Cat. No. 04906837001 Pack size 20 tablets (each for 10 ml) For more information visit: www.roche-applied-science.com/phoshataseinhibitor PHOSSTOP is a trademark of Roche.
84
3.1.

Inhibition of protease activity (see reference 1)
General Inhibitors for Classes of Proteases:

Serine proteasesa
PMSF Pefabloc SC Pefabloc SC PLUS Aprotinin Leupeptin+
2-Macroglobulin
Cysteine proteasesb
E-64
Metalloproteasesc
EDTA Phosphoramidon Bestatin (aminopeptidases
Aspartic proteasesd
Pepstatin
cpmplete, EDTA-free Protease Inhibitor Cocktail Tablets* cpmplete, Protease Inhibitor Cocktail Tablets* High-efficiency protease Inhibition a b c d + * Contain serine and histidine in the active center Contain cysteine (thiol, SH-) in the active center Contain metal ions (e.g., Zn2+, Ca2+, Mn2+) in the active center Contain aspartic (acidic) group in the active center Inhibits serine and cysteine proteases with trypsin-like specificity. When extractions or single-step isolations are necessary in the acidic pH range, include Pepstatin along with cpmplete Tablets to ensure aspartic (acid) protease inhibition.
3.1.
Inhibition of protease activity (continued) Protease-Specific Inhibitors:

Product Antipain dihydrochloride Calpain Inhibitor I Calpain Inhibitor II Chymostatin TLCK for the Inhibition of: Papain, Trypsin (Plasmin) Calpain I > Calpain II Calpain II > Calpain I Chymotrypsin Trypsin, other serine and cysteine proteases (e.g., Bromelain, Ficin, Papain) Trypsin
Trypsin-Inhibitor (chicken egg white, soybean)
85
3.1.
General

Stabilization
Low molecular weight substances such as glycerol or sucrose can help stabilizing proteins. However, care has to be taken when choosing these reagents since they can alter the activity of the protein of interest: e. g. sucrose and Poly Ethylene Glycol (PEG) are good stabilizers for invertase, but have denaturing effects on lysozyme. Certain salts (anions and cations) can significantly stabilize proteins in solution. Effectiveness of the stabilization effect of ions (according to Hofmeister, see reference 12): (CH3)4N+ > NH+ > K+ > Na+ > Mg2+ > Ca2+ > Ba2+ 4 2 SO4 > Cl > Br > NO3 > ClO4 > SCN Note that the widely used stabilization reagent ammonium sulfate 2 contains two of the most effective stabilizing ions: NH+ and SO4 . 4
Addition of salts
Addition of proteins
Highly diluted protein solutions are generally unstable. If rapid concentration is not possible, other proteins (e.g., BSA, up to ~ 1%) may be added to stabilize the sample. Poly-alcohols, Mono- and Polysaccharides, neutral polymers and aminoacids are not strongly charged and may not affect enzyme activity. Typical concentrations for poly-alcohols and sugars are 10 40% (w/v). Use non-reducing sugars or corresponding sugar alcohols (e.g., glycerol, xylitol) to avoid inactivation of proteins by reaction between amino groups and reducing sugars. Polymers (e.g., Poly Ethylene Glycol, PEG) in a concentration range of 1 15% increase the viscosity of single phase solvents and help prevent aggregation. Amino acids without charge (glycine and alanine) can act as stabilizers in a concentration range of 20 to 500 mM. Related compounds such as -amino butyric acid (GABA) and trimethylamine N-oxide (TMAO) can also be used in a range of 20 to 500 mM.
Addition of osmolytes
86
3.1.

Stabilization (continued)
Addition of substrates and specific ligands
Addition of specific substrates, cofactors or competitive inhibitors to purified proteins often results in good stabilizing effects. The protein adopts a more tightly folded conformation thereby reducing the tendency to unfold and rendering it less susceptible to proteolytic degradation. Note that dialysis may be necessary to avoid carryover effects of the substrate or inhibitor when the protein is removed from storage for use in particular situations where maximal activity is desired. Metal ions activate molecular oxygen and as a result the oxidation of thiol groups of cysteine residues. Complexation of these metal ions with e.g., EDTA leads to stabilization of proteins. Destructive oxidative reactions of thiol groups of cysteine can also be prevented by adding reducing agents such as -mercaptoethanol or dithiotreitol.
Addition of reducing agents
-Mercaptoethanol (-ME): Add -ME to a final concentration of 5 20 mM and keep if possible solution under anaerobic conditions (e.g., via an inert gas). -ME can form disulfide bridges with thiol groups of proteins leading to aggregation and/or inactivation. At pH 6.5 and 20C, the half-life of -ME is more than 100 hours. At pH 8.5 and 20C, the half-life decreases to 4 hours. Dithiotreitol (DTT): DTT is effective at lower concentrations ranging from 0.5 1 mM. The concentration should not exceed 1 mM, because it can act as denaturant at higher concentrations and is not soluble in high salt. Oxidation of DTT forms internal disulfide bridges resulting in deactivation, but does not interfere with protein molecules. At pH 6.5 and 20C, the half-life of DTT is 40 hours. At pH 8.5 and 20C, the half-life decreases to 1.4 hours.
87
3.2.
Conversion from Nucleic Acids to Proteins

Information transfer (see reference 2)
Since there are 43 = 64 possible nucleotide triplets, but only 20 amino acids plus some stop codons, most amino acids are encoded by several nucleotide triplets (synonyms, at maximum 6 in the cases of Arg, Leu and Ser). Most variants occur in the 3rd position of the code (Wobble hypothesis). The code is therefore called degenerate. The relationship between triplets and encoded amino acids is shown in the figure on the next page.
Notes
88
3.2.

The Genetic Code (see reference 2)
The triplet sequence is read from the center outwards. The mRNA nucleotide terminology is shown. For DNA nucleotide sequences, replace U with T. Basic amino acids are shown in blue, acidic amino acids in red, neutral amino acids in black and amino acids with uncharged, polar residues in orange.
Although the code has been assumed to be universal among living species, several exceptions in mitochondria have been found. Furthermore, in mycoplasma, UGA codes for Trp, while in some ciliated protozoa, the normal stop codons UAG and UAA specify Gln and UGA specifies Cys instead. Codon differences in Mitochondria:
UGA General Code Mitochondria Mammals Drosophila Protozoa Higher Plants S. cerevisiae Trp Met/ start Thr Trp Trp Trp Trp Met/ start Met/ start Stop Ser (AGA only) Stop AUA Ile CU(A,C,G,U) Leu AG(A,G) Arg CGG Arg General code Eukarya Bacteria
Codons with special functions:

Start Codons AUG (codes also for Met) Stop Codons UAG, UAA, UGA (amber, ochre, opal)
AUG (codes also for Met), CUG UAG, UAA, UGA (rare), ACG (rare), GUG (rare) AUG, GUG, UUG (rare) UAG, UAA, UGA AGA, AGG (mammals)
MitoAUA (codes also for Met), chondria AUG
89
3.2.

Characteristics of Amino Acids
Symbol A Ala R Arg N Asn D Asp C Cys Q Gln E Glu G Gly H His I Ile L Leu K Lys M Met F Phe P Pro S Ser T Thr W Trp Y Tyr V Val MW (in Da) Side group 89 -CH3 174 -(CH2)3-NH-CNH-NH2 132 -CH2-CONH2 133 -CH2-COOH 121 -CH2-SH 146 -CH2-CH2-CONH2 147 -CH2-CH2-COOH 75 -H 155 -C3N2H3 131 -CH(CH3)-CH2-CH3 131 -CH2-CH(CH3)2 146 -(CH2)4-NH2 149 -CH2-CH2-S-CH3 165 -CH2-C6H5 115 -C3H6 105 -CH2-OH 119 -CH(CH3)-OH 204 -C8NH6 181 -CH2-C6H4-OH 117 -CH-(CH3)2 GCU CGU AAU GAU UGU CAA GAA GGU CAU AUU CUU AAA AUG UUU CCU UCU ACU UGG UAU GUU GCC CGC AAC GAC UGC CAG GAG GGC CAC AUC CUC AAG UUC CCC UCC ACC UAC GUC Genetic code GCA GCG CGA CGG
Amino acid Alanine Arginine Asparagine Aspartic acid Cysteine Glutamine Glutamic acid Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptophan Tyrosine Valine
AGA
AGG
GGA AUA CUA
GGG
CUG
UUA
UUG
CCA UCA ACA
CCG UCG ACG
AGU
AGC
GUA
GUG
Basic amino acids are shown in blue, acidic amino acids in red, neutral amino acids in black and amino acids with uncharged, polar residues in yellow. Average molecular weight of amino acid: 110 Daltons.
Notes
90
3.2.

Codon Usage
Rarest codons (from E.coli) preferred by selected organisms:
Codon frequencies are expressed as codons used per 1000 codons encountered. A complete compilation of codon usage of the sequences placed in the gene bank database can be found at http://www.kazusa.or.jp/codon/ Codon frequencies of more than 15 codons/1000 codons are shown in bold to help identify a codon bias that may cause problems for high level expression in E. coli. The arginine codons AGG and AGA are recognized by the same tRNA (product of argU gene) and should therefore be combined. However, regardless of the origin of the coding region of interest, each gene should be addressed individually.
AGG arginine Escherichia coli Homo sapiens Drosophila melanogaster Caenorhabditis elegans Saccharomyces cerevisiae Plasmodium falciparium Clostridium pasteurianum Thermus aquaticus Arabidopsis thaliana 1.4 11.0 4.7 3.8 21.3 26.6 2.4 13.7 10.9
AGA arginine 2.1 11.3 5.7 15.6 9.3 20.2 32.8 1.4 18.4
CGA arginine 3.1 6.1 7.6 11.5 3.0 0.5 0.8 1.4 6.0
CUA leucine 3.2 6.5 7.2 7.9 13.4 15.2 6.0 3.2 9.8
AUA isoleucine 4.1 6.9 8.3 9.8 17.8 33.2 52.5 2.0 12.6
CCC proline 4.3 20.3 18.6 4.3 6.8 8.5 1.0 43.0 5.2
91
3.3.
Analyzing Proteins
Separation ranges of proteins in denaturing SDS-PAGE*
% Acrylamide** 6% 200 kDa 100 kDa 90 kDa 80 kDa 8% 10% 12% 15%
Range of separation of proteins
70 kDa 60 kDa 50 kDa 40 kDa 30 kDa 20 kDa 10 kDa 0 kDa
* Glycin buffer ** Molar ratio of acrylamide:bisacrylamide is 29:1.
Please refer to chapter 5 Preparing Buffers and Media for recipes to prepare denaturing SDS PAGE gels.
Sizes of commonly used markers in denaturing SDS-PAGE

Marker Myosin heavy chain (rabbit muscle) -Galactosidase (E.coli) Phosphorylase b (rabbit muscle) Fructose 6 phosphate kinase (rabbit muscle) Bovine Serum Albumin Glutamate dehydrogenase (bovine liver) Aldolase (rabbit muscle) Triose phosphate isomerase (rabbit muscle) Trypsin inhibitor (hen egg white) Trypsin inhibitor (soybean) Lysozyme (hen egg white) Cytochrome c (horse heart) Aprotinin Insulin chain B Molecular Weight (in kDa) 205 116 97.4 85.2 66.2 55.6 39.2 26.6 28.0 20.1 14.3 12.5 6.5 3.4
92
3.3.
Method
Analyzing Proteins
Staining of proteins on denaturing SDS-PAGE gels
Detection limit 300 1,000 ng per band
Coomassie Brilliant Blue R 250 Staining Standard Method Coomassie Brilliant Blue R 250 Staining Maximal Sensitivity Silver Staining Neutral Silver Staining Silver Staining Ammonium Silver Staining Copper Staining
50 100 ng per band
1 10 ng per band
1 10 ng per band
10 100 ng per band for 0.5 mm gels 1,000 ng per band for 1 mm gels 3 ng per band 1 2 ng per band
Staining with colloidal gold Staining with SYPRO fluorescent dyes
Please refer to Harlow and Lane: Antibodies, a Laboratory Manual, page 649 654 for the recipes of these staining techniques.
Staining and detection of proteins on membranes*

Staining Method Amido Black Detection limit ~ 2,000 ng NC Nylon PVDF Destaining NC PVDF Immunodetection NC PVDF
Ponceau S Coomassie Blue R 250
1,000 2,000 ng
500 1,000 ng
300 500 ng
India Ink
10 20 ng
Colloidal Gold
3 ng
NC = nitrocellulose PVDF = polyvinylidene difluoride * Products available from Roche Applied Science
93
3.3.
Analyzing Proteins
Buffer exchange via gel filtration
Matrix G 25 Material Dextran pH stability (in aqueous buffer) 2 10 Separation range in kDa (for globular proteins) 15 1.5 30 3 80 Agarose 3 13 10 4,000 60 20,000 70 40,000 Agarose/Dextran 3 12 0 10 3 70 10 600 Dextran/Bisacrylamide 3 11 1 100 5 250 10 1,500 Polyacrylamide 2 10 0.1 1.8 0.8 4 1.5 20 3 60 5 100
Sephadex
G 50 G 75 6B
Sepharose
4B 2B 30
Superdex
75 200 S 100HR
Sephacryl
S 200HR S 300HR P2 P4
Biogel
P 10 P 60 P 100
Properties of commonly used detergents: Definitions (see reference 3) Definitions
The MWCO (Molecular Weight Cut Off) is the minimum molecular weight of a molecule that will be retained by the membrane of the dialysis tubes. The minimum concentration at which detergents begin to form micelles. In practice, the CMC is the maximum concentration of detergent monomers that can exist in H2O. The CMC of a detergent may be changed by pH, temperature and the ionic strength of the solution. The CMC affects the dialysis of a non-ionic detergent. A detergent with a high CMC (and no ionic charge) is readily removed from detergent protein complexes by dialysis, whereas a detergent with a low CMC dialyzes away very slowly. Molecular weight of the detergent in its monomeric form.
Critical micellar concentration (CMC) (in mM)
Monomeric molecular weight (MMW) (in Da)
94
3.3.
Analyzing Proteins
Properties of commonly used detergents: Definitions (continued)
Micellar molecular weight (MMr) (in Da)
The average size of 1 micelle of a detergent (AuS). AuS = MMW x aggregation number (= average number of monomers in one micelle). In general, a detergent with a low CMC will have a high micellar molecular weight while a detergent with a high CMC will have a low micellar molecular weight.
Characteristics of detergents
Detergent Anionic SDS (Sodium dodecylsulfate) DOC (Deoxycholic acid) Zwitterionic CHAPS (3-[(3-Cholamidopropyl) dimethylammonio]-1-propanesulfonate) Nonionic Nonidet P-40 [Ethylphenolpoly (ethyleneglycolether)n] n-Octylglucoside CMC MMW MMr Working Ease of Application concentration removal > 10 mg per mg protein 0.1 10 mg membrane lipid 6.5 13 mM Good denaturing agent for proteins. Ideal for PAGE Solubilization of membrane proteins
8.3 14
288.4 416.6
18,000 4,200
614.9
6,150
Solubilization of membrane proteins.
0.25 14.5
606.6 (n = 11) 292.4
90,000
110 mM 46 mM
Protein solubilization Mild, non-denaturing detergent for the solubilization and reconstitution of membrane proteins. Easily removed via dialysis. Gentle solubilization and stabilization of membrane proteins Solubilization of proteins and PAGE Used for ELISA and Immunoblots
Sucrose monolaurate Triton X-100 [Octylphenolpoly (ethyleneglycolether)n] Tween 20 [Poly(oxyethylene)n sorbitan-monolaurate]
0.2 0.2 0.06
524.6 647 (n = 10) 1228 (n = 20) 90,000
0.2% 5% (w/v) 13.5 > 10 mg/mg membrane lipid
95
3.3.
Analyzing Proteins
Removal of detergents
Removal of detergents from protein solutions depends on three different variables: the physical properties of the detergent the characteristics (e.g., hydrophobic/hydrophilic) of the protein the components of the buffer system
Ionic detergents
Add urea to 8 M, then bind detergent to an ion exchange column. The protein will flow through in 8 M urea, then dialyze to remove urea. Gel filtration via a G-25 column. For some proteins, the column should be equilibrated in another detergent below its CMC. For ionic detergents with a relatively low micellar size and low CMC: dilute the sample as much as possible and dialyze. Add a mixed bed resin to the dialysate to increase the exchange rate. Gel filtration via a G-200 column. Dilute the sample and dialyze against deoxycholate, then remove deoxycholate by dialysis. Velocity sedimentation into sucrose without detergent. Bind protein to an affinity matrix or ion exchange column, wash to remove detergent and elute protein. For some proteins, the column should be equilibrated in another detergent below its CMC.
Non-ionic detergents
Ammonium sulfate precipitation
Amounts of ammonium sulfate (in g/l solution) to change the concentration of a solution from a initial percentage of saturation to a desired target percentage saturation at 0C:
Target percentage saturation
Initial percentage saturation
0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 20 106 79 53 26 25 134 108 81 54 27 30 164 137 109 82 55 27 35 194 166 139 111 83 56 28 40 226 197 169 141 113 84 56 28 45 258 229 200 172 143 115 86 57 29 50 291 262 233 204 175 146 117 87 58 29 55 326 296 266 237 207 179 148 118 89 59 30 60 361 331 301 271 241 211 181 151 120 90 60 30 65 398 368 337 306 276 245 214 184 153 123 92 61 31 70 436 405 374 343 312 280 249 218 187 156 125 93 62 31 75 476 444 412 381 349 317 285 254 222 190 159 127 95 63 32 80 516 484 452 420 387 355 323 291 258 226 194 161 129 97 65 32 85 559 526 493 460 427 395 362 329 296 263 230 197 164 132 99 66 33 90 603 570 536 503 469 436 402 369 335 302 268 235 201 168 134 101 67 34 95 650 615 581 547 512 478 445 410 376 342 308 273 239 205 171 137 103 68 34 100 697 662 627 592 557 522 488 453 418 383 348 313 279 244 209 174 139 105 70 35
Add step by step small portions of the required amount of ammonium sulfate allowing to dissolve each portion before the next portion is added. This will prevent accumulation of undesirable high local salt concentrations.
96
3.3.
Analyzing Proteins
Other precipitation techniques
Trichloroacetic acid (> 5 g/ml)
Add equal volume of 100% trichloroacetic acid (TCA) to the sample and vortex. Leave for 20 minutes on ice or for 15 minutes at 20C. Centrifuge for 5 min at 6,000 10,000 g. Remove the supernatant. Resuspend the pellet with 0.1 M NaOH or wash the pellet with an ethanol/ether (1/1) solution and resuspend the pellet in a buffer solution. Add 5 volumes of cold ( 20C) aceton to the sample and vortex. Leave for 30 min at 20C. Centrifuge for 5 min at 6,000 10,000 g. Remove the supernatant and let the pellet air dry. Resuspend the pellet in buffer. Add 3 volumes of methanol and 1 volume of chloroform to the sample and vortex. Add 3 volumes H2O, vortex for ~ 1 minute. Centrifuge for 5 min at 6,000 10,000 g and discard the upper phase. Add 3 volumes of methanol and vortex. Centrifuge for 5 min at 6,000 10,000 g. Remove the supernatant and let pellet air dry. Resuspend the dry pellet in buffer.
Aceton precipitation (< 1 g/ml)
Chloroform-Methanol precipitation ( 1 g/ml)
Notes
97
3.4.
Quantification of Proteins
OD Measurement
Read the absorbance of the protein solution versus a suitable control (solvent blank) at 280 nm or 205 nm. A rough approximation for proteins is: 1 A280 Unit of proteins = 1 mg/ml. (for ranges of protein concentrations from 20 to 3000 g/ml) Typical A280 values for 1 mg/ml protein are : BSA: IgG: IgM: 0.70 1.35 1.20
Pure protein solutions
(Samples with absorbance > 2.0 should be diluted in the appropriate solvent to obtain absorbances < 2.0).
Protein concentration (in mg/ml) = A205/31 (for ranges of protein concentrations from 1100 g/ml) Protein solutions contaminated with nucleic acids (nucleic acid content up to 20% w/v or A280/A260 < 0.6) Read the absorbance versus a suitable control (e.g., buffer blank) at 280 nm and 260 nm or 280 nm and 205 nm. Calculate the approximate concentration using one of the following equations: Protein concentration (in mg/ml) = (1.55 x A280) (0.76 x A260) Protein concentration (in mg/ml) = A205/(27 + A280/A205) Protein/DNA conversions (1 kb of DNA encodes 333 amino acids = 3.7 x 10 4 Da) Protein 10 kDa 30 kDa 100 KDa DNA 270 bp 810 bp 2.7 kbp
Molar conversions for Proteins 100 pmol Protein 10 kDa 30 kDa 100 kDa g Protein 1 3 10
Assays Lowry method Reagent A:
Dissolve 10 g Na2CO3 in 500 ml H2O. Dissolve 0.5 g CuSO4 5H2O and 1 g Na-tartrate in 500 ml of H2O. Add the Na2CO3 solution slowly to the copper/tartrate solution on a magnetic stirrer. This solution can be stored at 4C for one year. Combine one volume of the reagent A with 2 volumes of 5% SDS and 1 volume of 0.8 M NaOH. This solution is stable at room temperature for 2 weeks.
Before usage: Reagent Aactivated
Reagent B:
Combine 1 volume of 2 N Folin-Ciocalteau Phenol reagent with 5 volumes H2O. This solution is stable for several months in a dark bottle at room temperature. Prepare samples of 100, 50, 25 and 12.5 g/ml BSA in H2O. Add 1 ml of reagent Aactivated, mix and incubate for 10 min at room temperature. Add 0.5 ml of Reagent B, mix immediately and incubate at room temperature for 30 min. Read absorbance at 750 nm, prepare a linear standard curve and calculate concentration.
98
3.4.
Assays (continued)
Bicinchoninic acid method
Reagent A and reagent B are commercially available. Mix 1 volume of reagent A to 50 volumes of reagent B. Prepare samples of 100, 50, 25 and 12.5 g/100 l of BSA. Add 2 ml of the combined reagent to each sample and incubate for 30 min. at 37C. Read the samples versus an appropriate blank at 562 nm. Prepare a linear standard curve and calculate concentration. Dissolve 100 mg Coomassie brilliant blue G250 in 50 ml 95% ethanol. Add 100 ml concentrated phosphoric acid. Add H2O to a final volume of 200 ml. The Bradford dye concentrate is stable for 6 months at 4C. Prepare samples of 100, 50, 25, and 12.5 g/100 l in the same buffer solution as your protein sample. Dilute the Bradford dye concentrate 5 x with H2O, filter if precipitation occurs. Add 5 ml of the diluted dye to each sample. The red dye will turn blue when binding to the protein, allow color to develop for at least 5 min, not longer than 30 min. Read the absorbance at 595 nm, prepare a linear standard curve and calculate concentration.
Bradford method
Biuret method
Biuret Reagent: Dissolve 1.5 g CuSO4 5H2O and 6 g sodium potassium tartrate in 500 ml of water. Add 300 ml 10% (w/v) NaOH and make up to 1 liter with H2O. Store in a plastic container in the dark. This solution will keep indefinitely if 1 g of potassium iodide is added to inhibit the reduction of copper. Prepare samples with 0.5, 1.0, 1.5, 2, 2.5 and 3 mg of BSA. Add 2.5 ml of Biuret reagent, allow to react for 30 min. Measure absorbance at 540 nm against a blank containing 0.5 ml of sample buffer plus 2.5 ml of Biuret reagent. Prepare a linear standard curve and calculate concentration. Note that this test has a low sensitivity (range 1 6 mg protein/ml).
99
3.4.
Concentration limits of interfering reagents for assays
Use this chart to select the appropriate wavelength depending on the contents of your buffer:
Reagents Ammonium sulfate Brij 35 DTT EDTA Glycerol KCl -ME NaCl DTT: EDTA: -ME: SDS: TCA: A205 9% (w/v) 1% (v/v) 0.1 mM 0.2 mM 5% (v/v) 50 mM <10 mM 0.6 M dithiothreitol ethylenediaminetetraacetic acid -mercaptoethanol sodium dodecylsulfate trichloroacetic acid A280 > 50% (w/v) 1% (v/v) 3 mM 30 mM 40% (v/v) 100 mM 10 mm >1M Reagents NaOH Phosphate buffer SDS Sucrose Tris buffer Triton X-100 TCA Urea A205 25 mM 50 mM 0.1% (w/v) 0.5 M 40 mM < 0.01% (v/v) < 1% (w/v) < 0.1 M A280 >1M 100 mM 0.1% (w/v) 2M 0.5 M 0.02% (v/v) 10% (w/v) >1M
Compatibility of different buffer systems with protein quantification assays

BCA ACES ADA BES Bicine Bis-Tris CAPS CHES DIPSO Glycine HEPES HEPPS Lowry Bradford HEPPSO MES MOPS MOPSO PIPES POPSO TAPS TAPSO TES Tricin Tris BCA Lowry Bradford
* Please also note the overview regarding pH buffering ranges in section 5.1, Buffer page 148.
100
3.4.
Compatibility of different buffer systems with protein quantification assays (continued)
Abbreviations
ACES (N-(2-Acetamido)-2-aminoethanesulfonic acid) ADA (N-(2-Acetamido)(2-iminodiacetic acid) BES (N,N-bis-(2-hydroxyethyl)-2-aminoethanesulfonic acid) Bicine (N,N-bis-(2-hydroxyethyl)-glycine) Bis-Tris (bis-(2-hydroxyethyl)-iminotris-(hydroxymethyl)-methane) CAPS (3-Cyclohexylamino)-1-propansulfonic acid) CHES (2-(N-Cyclo-hexylamine)-ethanesulfonic acid) DIPSO (3-N,N-Bis-(2-hydroxyethyl)-3-amino-2-hydroxypropanesulfonic acid) HEPES 4-(2-hydroxyethyl)-piperazine-1-ethanesulfonic acid) HEPPS (4-(2-hydroxyethyl)-piperazine-1-propanesulfonic acid) HEPPSO (4-(2-hydroxyethyl)-piperazine-1(2-hydroxypropanesulfonic acid) MES (2- Morpholinoethanesulfonic acid) MOPS (3-Morpholinopropanesulfonic acid) MOPSO (3-Morpholino-hydroxypropanesulfonic acid) PIPES (Piperazine-1, 4-bis-(2-ethanesulfoic acid) POPSO (Piperazine-1, 4-bis-(2-hydroxypropanesulfonic acid)) TAPS (N-[Tris-(hydroxymethyl)-methyl]-3-aminopropanesulfonic acid) TAPSO (N-[Tris-(hydroxymethyl)-methyl]-3-amino-2-hydroxypropanesulfonic acid) TES (N-[Tris-(hydroxymethyl)-methyl]-2-aminoethanesulfonic acid) Tricin (N-[Tris-(hydroxymethyl)-methyl]-glycine)
Notes
101
3.5.
Purifying Proteins
Characteristics of different expression systems
E. coli Yeast Mammalian cells Insect cells RTS*
Characteristics Expression of toxic proteins Expression from PCR templates Proteolytic cleavage**** Glycosylation Secretion Folding Phosphorylation Percentage Yield (dry weight) Labeling * ** *** ****
** *** 1 5% 1% < 1% 30% up to 6 mg/ml
Rapid Translation System available from Roche Applied Science (please refer to p. 103) with chaperones with suitable kinase and substrate inhibited by e.g. cpmplete Protease Inhibitor Cocktail Tablets
Sources of antibodies
Source Type Quantity of total antibody 10 mg/ml Quantity of Contaminating specific antibody antibodies < 1 mg /ml Other serum antibodies Purity of specific antibody 10% (except for antigen affinity column) > 95%, no cross reaction high quality > 95%, no cross reaction high quality Max. 90%, cross reactions possible Comments
Serum
Polyclonal
Antigen-affinity purification procedure
Culture supernatant with 10% FCS
Monoclonal
1 mg/ml
0.01 0.05 mg/ml
Background from calf serum
Purification with protein A or G columns* Purification with protein A or G columns* Antigen affinity purification procedure
Culture supernatant with serum-free medium Ascites
Monoclonal
0.05 mg/ml
0.05 mg/ml
None
Monoclonal
1 10 mg/ml
0.9 9 mg/ml
Background from mouse antibodies
* not recommended for IgM.
102
3.5.
Purifying Proteins
Expressing Proteins: Cell-free - Rapid Translation System
The Rapid Translation System (RTS) from Roche Applied Science is a scalable in vitro protein expression platform that produces large amounts of protein for characterization studies, functional assays, or structural analysis. It is available based on bacterial (E. coli) as well as eukaryotic (wheat germ) cell lysates. RTS enables both transcription and translation utilizing the unique HY (High-Yield) and the patented CECF (continuous-exchange, cell-free) technologies. RTS offers much higher levels of protein expression compared to other in vitro transcription/translation systems, with yields of up to 6 mg/ml of expressed protein.
Fig. 1: Schematic illustration of the continuousexchange cell-free (CECF) reaction principle
Fig. 2: GFP (Green Fluorescent Protein) expression compared to a conventional in vitro expression system
Transcription and translation take place simultaneously in the reaction compartment. Substrates and energy components needed for a sustained reaction are continuously supplied through a semi-permeable membrane. Potential inhibitory reaction by-products are diluted via diffusion through the same membrane into the feeding compartment. High levels of protein expression by allowing protein synthesis to continue for up to 24 hours. Conquer complex problems with ease Expression of several DNA templates in a single reaction to express proteins in parallel Overcome the limitations of cell-based systems by expressing toxic proteins in a cell-free RTS lysate. Elimination of laborious up- and downstream steps (e.g., host-cell transformation, culturing, or lysis) Expression of proteins from PCR-generated linear templates or suitable expression vectors
103
3.5.
Purifying Proteins
Expressing Proteins: Cell-free - Rapid Translation System (continued)
Prokaryotic cell-free expression kits RTS 100 E. coli HY Kit RTS 100 E. coli Disulfide Kit RTS 500 E. coli Disulfide Kit RTS 500 ProteoMaster E. coli HY Kit RTS 9000 E. coli HY Kit
mg/ml up to 0.4 mg/ml up to 1.5 mg/ml up to 2.5 mg/ml up to 6 mg/ml up to 5 mg/ml
mg/l reaction up to 0.02 mg/50 l up to 0.08 mg/50 l up to 2.5 mg/1 ml up to 6 mg/1 ml up to 50 mg/10 ml
hours 4 24 24 24 24
Eukaryotic cell-free expression kits RTS 100 Wheat Germ CECF Kit RTS 500 Wheat Germ CECF Kit
mg/ml up to 1 mg/ml up to 1 mg/ml
mg/l reaction up to 0.05 mg/50 l up to 1 mg/1 ml
hours 24 24
The RTS E. coli Disulfide and RTS Wheat Germ Kits allow the expression of soluble disulfide-bonded or eukaryotic proteins with high success rates.
If your protein is eukaryotic and ... didnt express in E. coli in vitro you want a high initial success rate didnt express in RTS E. coli isnt soluble when expressed in E. coli (RTS or in vivo) needs disulfide bonds doesnt depend on correct folding for downstream applications needs to be glycosylated If your protein is prokaryotic and ... doesnt depend on correct folding for downstream applications you want a high initial success rate needs disulfide bonds
you should use ... RTS Wheat Germ RTS Wheat Germ RTS Wheat Germ RTS Wheat Germ RTS E. coli Disulfide RTS E. coli a cell-based system you should use ... RTS E. coli RTS E. coli after sequence optimization with ProteoExpert RTS E. coli Disulfide
or alternatively use ... RTS E. coli RTS E. coli after sequence optimization with ProteoExpert
or alternatively use ... RTS Wheat Germ
Many prokaryotic, eukaryotic, and viral proteins have already been expressed with RTS.
For the most current list of successfully expressed proteins and for further information please visit: www.proteinexpression.com
104
3.5.
Animal
Purifying Proteins
Choices of animals for immunization
Maximal amount of serum* ~ 500 ml ~ 2 ml ~ 20 ml ~ 20 ml ~ 30 ml ~ 20 ml /egg Possibility to generate monoclonal antibodies Inbred Comments
Rabbits Mice Rats Hamsters Guinea Pigs Chicken
Best choice for polyclonal antibodies Best choice for monoclonal antibodies Good choice for monoclonal antibodies Good choice for polyclonal antibodies Hard to bleed Antibodies are available during entire life of chicken
* during the course of one immunization regime
Notes
105
3.5.
Purifying Proteins
Doses of immunogens for Rabbits
Examples Enzymes Carrier proteins conjugated with peptides Immune complexes Routes of injections Subcutaneous Intramuscular Intradermal Intravenous Subcutaneous Intramuscular Intradermal Dose 50 1 000 g
Type of antigen Soluble Proteins
Particulate Proteins
Viruses (killed) Yeast (killed) Bacteria (killed) Structural proteins Bacterially produced from inclusion bodies Immunopurified proteins bound to beads
50 1 000 g
Insoluble Proteins
Subcutaneous Intramuscular Intradermal Subcutaneous Intramuscular Intradermal Intravenous Subcutaneous Intramuscular Intradermal Intravenous
50 1 000 g
Carbohydrates
Polysaccharides Glycoproteins
50 1 000 g
Nucleic acids
Carrier proteins conjugated to nucleic acids
50 1 000 g
Routes of injections for Rabbits

Routes Subcutaneous Maximum volume 800 l per site, 10 sites per animal 500 l 100 l per site, 40 sites per animal 1 000 l Adjuvant Possible Immunogen Soluble or insoluble Comments Easy injections
Intramuscular Intradermal
Possible Possible
Soluble or insoluble Soluble or insoluble
Slow release Injections more difficult, slow release Not effective for primary immunizations
Intravenous
No
Soluble, ionic detergent < 0.2% Non ionic detergent < 0.5% Salt < 0.3 M Urea < 1 M
106
3.5.
Purifying Proteins
Purifying antibodies using Protein A*, Protein G* and Protein L
Use this chart to select the appropriate product to purify antibodies from solutions:
Organism Human Antibody IgG1 IgG2 IgG3 IgG4 IgM IgA IgE IgD Fab F(ab)2 k light chain scFv Mouse IgG1 IgG2a IgG2b IgG3 IgM Protein A ++ ++ ++ + + + + + + ++ ++ + Protein G ++ ++ ++ ++ + + ++ ++ ++ + Protein L ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ ++ = strong binding + = moderate binding = no binding Goat Chicken Cow Rabbit Horse Pig Sheep Organism Rat Antibody IgG1 IgG2a IgG2b IgG2c IgG IgG IgG IgG1 IgG2 IgG IgY IgG1 IgG2 Protein A + ++ + ++ +/++ ++ Protein G + ++ + ++ ++ ++ ++ ++ ++ ++ ++ ++ Protein L ++ ++ ++ ++ + ++ ++
* Protein A Agarose (Cat. No. 11 134 515 001) and G Agarose (Cat. No. 11 243 233 001) are available from Roche Applied Science
Immunoprecipitation Cell Preparation
Wash cells/tissue at least twice with ice-cold PBS to remove remaining serum proteins from the culture medium. A sample volume of 1 to 3 ml per immunoprecipitation reaction is recommended. Composition of 1 x lysis buffer: 50 mM Tris, pH 7.5; 150 mM NaCl 1% Nonidet P40; 0.5% sodium deoxycholate a 1 Complete Protease Inhibitor Cocktail Tablet per 25 to 50 ml buffer Stability of lysis buffer: stable for 24 hours at 4C stable in aliquots for at least 4 weeks at 20C.
Cell Lysis
Product available from Roche Applied Science: Complete e.g., Cat. No. 04 693 116 001 (more details in reference 14)
107
3.5.
Note
Purifying Proteins
Immunoprecipitation (continued)
In rare cases, aspartic acid proteases can interfere during isolations in animal tissues. These proteases however only exhibit pronounced activities in the acid pH range. If extractions have to be performed at these pH values, it is recommended to add pepstatin* to the above lysis buffer at a concentration of 0.7 g/ml. Detergents are essential for breaking up the cells and keeping proteins in a soluble state. In most cases, the detergents included in the above mentioned lysis buffer are suitable. However, for some antigens, more sophisticated solubilization protocols may be applied when the protein has to be obtained in a functionally active state. Low salt wash buffer: same buffer as lysis buffer High salt wash buffer (1x concentrated): 50 mM Tris, pH 7.5 500 mM NaCl 0.1% Nonidet P40 0.05% sodium deoxycholate
Wash Buffers
Stability of wash buffers: stable for 24 hours at 4C stable in aliquots for at least 4 weeks at 20C. Add 20% glycerol to these wash buffers if solutions need to be stored at 20C. Note: The tighter the binding between antibody and antigen, the more stringent the washing conditions should be. The washing buffers described are used if low stringency conditions are appropriate. If higher stringency is required, increase salt concentrations and ionic strength by using 0.5 M NaCl or 0.5 M LiCl in the first wash. Additionally, 0.1% SDS may be applied during cell lysis and the first two washes.
Tips
Keep temperature during the whole procedure between 0 and 4C to help to reduce enzymatic degradation.
* Available from Roche Applied Science Cat. No. 10 253 286 001 2 mg; Cat. No. 11 359 053 001 10 mg; Cat. No. 11 524 488 001 50 mg
108
3.5.
Purifying Proteins
Ion Exchange Chromatography
Principle
Ion exchange chromatography depends on the reversible absorption of charged solute biomolecules to immobilized ion exchange groups. Every soluble biomolecule will have a specific interaction with the resin, depending on its charge under the choosen pH and counterionconditions. These conditions have to be established experimentally to find the optimal proportions to elute the molecule of interest from the resin. Neutralizing the ionic interactions with counterions like salts or by changing the pH desorbs the molecule from the resin. There exist two types of ion exchange groups: Anion exchangers with the charged groups Diethylaminoethyl (DEAE, weak anion exchanger) and Quaterny ammonium (Q, strong anion exchanger) Cation exchangers with the charged groups Carboxymethyl (CM, weak kation exchanger) and Sulphopropyl (SP, strong kation exchanger). Strong ion exchangers are more stable in their behavior under different pH conditions.
Types
These groups are coupled to a broad variety of immobile phases that define the ligand density and the physical and chemical properties of the resin. For a more comprehensive overview of the different types of commercially available products, please refer to references 4, 7, 9, 10 and the product specifications of the different manufacturers of columns and media.
109
3.5.
Purifying Proteins
Ion Echange Chromatography: Experimental setup
An easy setup experiment for establishing chromatographic conditions for proteins:
1. Adjust the pH of the sample in 0.5 pH steps between pH 6 and pH 9 2. Incubate 20 l of the sample with 10 l chromatographic resin, equilibrated at the same pH and buffer conditions, for 10 minutes at an appropriate temperature with careful mixing. 3. Spin down the chromatographic resin in a desk-top centrifuge. 4. Test the supernatant for the protein in comparison to the load, measure the total content of the supernatant. 5. Choose the pH at which the protein of interest binds to the resin (nothing in the supernatant) and desirably most of the total protein is in the supernatant and test under which counterion conditions the protein will no longer bind to the resin: 6. Adjust the counterion (e.g., KCl or NaCl) concentration of the sample in 50 mM steps between 100 mM and 1 M.
7. Incubate 20 l of the sample with 10 l chromatographic resin, equilibrated to the same counterion concentration of the sample, for 10 minutes at an appropriate temperature with careful mixing. 8. Spin down the chromatographic resin in a desk-top centrifuge. 9. Test the supernatant for your protein in comparison to the load, measure the total content of the supernatant. 10. These test should be performed with different ion-exchangers to find the most optimal resin. You can also use the obtained information to find conditions where most contaminants bind but the protein of interest remains unbound, although the binding and elution from a resin is more desirable because it yields concentrated protein.
110
3.5.
Tag AviTag
Purifying Proteins
Tagging
Size 15 aa Remarks/Sequence Mono-biotinylation of proteins via the AviTag sequence/GLNDIFEAQKIEWHE Host Cleavage Detection via Immunoprecipita- Immuno affinity Western Blottion purification ting StreptavidinPOD* Streptavidin Mutein Matrix* Immunofluorescence
RTS* (Cell-free) None Mammalian cells Bacterial cells Insect cells Yeast Mammalian cells Enterokinase Bacterial cells Yeast Mammalian cells Factor Xa Bacterial cells Mammalian cells None
Streptavidin Mutein- Avidin-Fluorescein* or Matrix*. Lowered Avidin-Rhodamine* biotin dissociation -7 constant (1.3x10 M) allows elution of biotinylated proteins Anti-Flag agrose affinity gels APTG-Agarose Anti-GFP* Anti-Flag with secondary antibody Anti--gal with secondary antibody Direct green fluorescence of fused proteins or Anti-GFPFlourescein* antibody
Flag
8 aa
Synthetic peptide Sequence: DYKDDDDK -galactosidase
Anti-Flag
Anti-Flag
-gal GFP
120 kDa
Anti--gal Anti-GFP*
Anti--gal Anti-GFP*
27 kDa Green fluorescent protein
GST HA
26 kDa Glutathione-Stransferase 9 aa
Bacterial cells Insect cells
Thrombin Fac- Anti-GST tor Xa
GST-Agarose Beads
Glutathion-agarose- Anti-GST with seconbeads dary antibody Anti-HA-Biotin*, Flourescein* or Rhodamine*
Peptide of human influ- Mammalian cells None enza virus Bacterial cells Sequence: YPYDVPDYA
Anti-HA-POD* Anti-HA*, Anti-HA Anti-HA*, Anti-HA Affinity Matrix* Affinity Matrix* Anti-His6POD* Anti-His6*
His6 or His10
6 aa or Polyhistidine binds me- Mammalian Cells Thrombin 10 aa tal ligand (affinity chro- Bacterial cells enterokinase matography) Yeast Insect cells
Poly-His-Protein pu- Anti-His with secondary rification-Kit antibody
Tag Intein
Size
Remarks/Sequence
Host
Cleavage
Detection via Immunoprecipita- Immuno affinity Western Blottion purification ting Anti-Intein Chitin-beads
Immunofluorescence Anti-Intein with secondary antibody
55 kDa Protein splicing element Bacterial cells from the Yeast VMA 1 gene 44 kDa Maltose binding protein Bacterial cells 10 aa Human c-myc protein Sequence: EQKLISEEDL Ca2+ depending binding of Anti-Protein C antibody Sequence: EDQVDPRLIDGK
Mediated self- Anti-Intein cleavage Factor Xa Anti-MBP Anti-c-mycPOD* Anti-Protein C-POD
MBP c-myc
Amylose Resin Anti-c-myc* Anti-c-myc* Anti-c-myc with secondary antibody Anti-Protein C with secondary antibody
Mammalian cells None Bacterial cells Mammalian cells None Bacterial cells
Protein C 12 aa
Anti-Protein C, Anti-Protein C Affinity Matrix*
Anti-Protein C, Anti-Protein C Affinity Matrix*
VSV-G
11 aa
Vesicular Stomatitis Vi- Mammalian cells None rus Sequence: Bacterial cells YTDIEMNRLGK
Anti-VSV-GPOD
Anti-VSV-G*
Anti-VSV-G*
Anti-VSV-G with secondary antibody
* availabel from Roche Applied Science
111
3.6.
References
1. The Complete Guide for Protease Inhibition (2007) Roche Applied Science 2. Michal, G (2006) Biochemical Pathways: An atlas of Biochemistry and Molecular Biology, Spektrum Verlag, Heidelberg 3. Biochemica Information (1994) Roche Applied Science 4. Doonan, S. (1998) Protein Purification Protocols, Methods in Molecular Biology 5. Harlow, E. and Lane, D. (1988) Antibodies, a Laboratory Manual, Cold Spring Harbor Laboratory Press 6. Brown, T. A. (1991) In: Molecular Biology LabFax. Bios Scientific Publishers, Academic Press 7. Sambrook. J., Fritsch, E. J. and Maniatis, T. (1989) In: Molecular Cloning, A Laboratory Manual, 2nd edition. Cold Spring Harbor Laboratory Press 8. Roche Applied Science, Technical Data Sheets 9. Harris et al (1990) Protein Purification Applications, a practical approach, IRL Press 10. Wheelwright, S. (1991) Protein Purification, Hanser Publishers 11. Hofmeister, F. (1888) Arch. Exp. Path. Pharmakol. 24, 247 260 12. Rapid Translation System: Application Manual (2002) Roche Applied Science 13. Protein Expression and Analysis, Brochure (2005), Roche Applied Science
Working with Cells

Chapter 4
4.1. 4.2. 4.3. 4.4 4.5.
Precautions for handling Cells ................................... Basic Information ............................................................. Manipulating Cells .......................................................... Analyzing Cells ................................................................. References .........................................................................
113 117 123 131 144
4.1.
General
Precautions for handling Cells

Tissue culture reagents
Optimize growth conditions of your cells: use only fresh media and additives and minimize variations. Various commercial media are available (e.g., RPMI 1640, DMEM). Medium constituents are nutrients (amino acids, glucose), vitamins, inorganic salts and buffer substances. Some constituents are quite unstable and therefore may cause problems when not freshly added. Many cells need additional factors for proper growth. Serum is an extremely complex mixture of albumins, globulins, growth promotors and growth inhibitors. The quantity and quality of these components are affected by age, nutrition and health of the animals from which the serum is obtained. It is subject to significant biological variation. Some cells are dependent on additional substances/components which are neccessary for viability or dividing activity, e.g., growth factors, trace elements, essential metabolites, proteins.
Basic medium
Fetal calf serum
Additives
CO2 Incubator
Cells are grown at 37C in a CO2-incubator at 100% relative humidity. CO2 is needed to control pH. Cell physiology is highly sensitive to pH variations. Some media need a concentration of 5% CO2, other media have to be run at 10% CO2. Inconsistent conditions within an incubator may cause variances between culture plates. Pollution, chemicals, fungal or bacterial contamination's from the incubator may affect cell physiology.
Working with Cells
113
4.1.

Tissue culture reagents
Commonly used antibiotics in cell culture

Antibiotic Ampicillin* Amphotericine B* Cabenicillin Ciprofloxacin BM-Cyclin* (Pleuronutilin and Tetracyclin derivates) Erythromycin Gentamycin* Kanamycin* Lincomycin Neomycin Nystatin Penicillin G* Polymixin B Streptomycin*
a
Concentration a) 100 U/ml 0,25 to 25 g/ml 100 U/ml 10 g/ml 10 g/ml 5 g/ml 100 g/ml 5 to 50 g/ml 100 g/ml 50 g/ml 50 g/ml 100 U/ml 50 to 100 U/ml 100 U/ml 50 to 100 g/ml
Grampos.Bact. + + + + + + + + + +
Gramneg. Bact. + + + + + + + + +
Mycoplasm. + + + + +/-
Yeast + + + -
Fungi + + -
Stability at 37C 3 days 3 day 3 days 5 days 3 days 3 days 3 days 5 days 4 days 5 days 3 days 3 days 5 days 5 days
two or more antibiotics at the suggested concentration may cause cytopathic effects. * Product available from Roche Applied Science
Decontamination of cell culture:
1) 2) 3) 4) 5) 6)
Dilute and seed cells into 96 well plate with antibiotica free medium. Ad antibiotica at different concentrations. Check surviving rate at highest concentration of antibiotic. Reduce the concentration 1 to 2times in future treatments. Cultivate the cells in medium without antibiotic. Repeat step 1) to 5) until the culture is free of contamination.
Working with Cells
114
4.1.

Growth areas and yields of cellsa in a culture vessels
Growth areab (cm2) 96 well 48 well 0.32 0.6 1 2 4 9.5 8 21 56 145 25 75 162 175 225 Numbers of cellsc ~ 4 x 10 4 ~ 1 x 105 ~ 2.5 x 105 ~ 5 x 105 ~ 1 x 10 6 ~ 1 x 10 6 ~ 2.5 x 10 6 ~ 7 x 10 6 ~ 2 x 107 ~ 3 x 10 6 ~ 1 x 107 ~ 2 x 107 ~ 3 x 107
Cell Culture Vessel
Multiwell plates
24 well 12 well 6 well 35 mm 60 mm
Dishes 100 mm 145 150 mm 40 50 ml 250 300 ml Flasks 650 750 ml 900 ml
a b c
Such as 3T3, Hela or CHO cells. Per well, if multiwell plates are used; varies slightly depending on supplier. assuming confluent growth.
Mycoplasma Contamination Introduction
Mycoplasma is a common and serious contamination of cell cultures, and one of the major problems in biological research using cultured cells. It has been shown that up to 30% (variation from 5% to 85%) cell cultures are contaminated with mycoplasma, the main contaminants being the species M.orale, M.laidlawaii, M.arginii and M.hyorhinis. It is important to keep in mind that mycoplasma do not always reveal their presence with macroscopic alterations of the cells or medium. Many mycoplasma contaminants, particularly in continuous cell lines, grow slowly and do not destroy host cells. They are able, however, to affect various parameters (e.g., changes in metabolism, growth, viability, morphology, etc.) and thus can interfere with experiments in cell culture. Therefore, it is an absolute requirement for routine, periodic assays to detect possible contamination of cell cultures. This is particularly important with continuous or established cell lines. The major source of Mycoplasma contamination are: Cells purchased from outside People handling cells Serum, medium and additives Liquid nitrogen
Working with Cells
115
4.1.

Mycoplasma Contamination
Indication for Mycoplasma contamination

Cells not adhering to culture vessel Mycoplasma contamination Segregate culture and test for Mycoplasma infection. Clean fume hood and incubator.
Overlay trypsinized cells No attachemend factors in medium Decreased growth of culture Mycoplasma contamination Segregate culture and test for Mycoplasma infection. Clean fume hood and incubator.
Low level bacterial or fungi contamination Depletion, absence or breakdown of essential growth-promoting components. Inproper storage of reagents Very low initial cell inoculum
Suspension cells clumping together
Mycoplasma contamination
Segregate culture and test for Mycoplasma infection. Clean fume hood and incubator.
Presence of calcium and magnesium ions Cell lysis and release of DNA resulting from overdigestion with proteolytic enzymes
Detection of Mycoplasma contamination
Overview of different assays

Assay DNA staining with DAPI* DNA-RNA hybridisation ELISAa PCR
a
Sensitivity +/+ +/+ +/-
Specifity +/+ + + +/-
Culture
Working with Cells
116
4.1.
Assay

Detection of Mycoplasma contamination
Principle DAPI is a fluorescent dye that specifically stains double-stranded DNA
DAPI* (4',6-Diamide-2'-phenylindole dihydro chloride) Culture
Combination of direct mycoplasma cultivation in aerobic and anaerobic conditions. A species specific assay should follow the isolation. Determination of each species is use done seperatly. Usely multiplex PCR for the most "popular" mycoplasma strains.
ELISA** PCR*
a Mycoplasma Detection Kit (Cat. No. 11 296 744 001) and **Mycoplasma PCR ELISA (Cat. No. 11 663 925 910) are available from Roche Applied Science. * products available from Roche Applied Science.
Elimination of Mycoplasma in cell culture BM-Cyclin*: 510 g/ml medium Gentamycin*: 50 g/ml medium Ciprofloxacin: 10 g/ml medium
4.2.
Basic Information
Typical Properties of Bacterial Cells
Domain Kingdom Nucleus Genome RNA Polymerase Starting amino acid for translation Reproduction Cellular organization Nutrition Size of cells
Bacteria Bacteria no (common term prokarya) circular, ca. 10 6 to 5 x107 kb, extra plasmids one type formylmethionine binary scission unicellular (some are aggregated) chemoorganotrophic, photoautotrophic or photoheterotrophic average 1 5 m, wide variation rigid, contain peptidoglycans no
After Campbell, N.A.: Biology 4/e. Benjamin/Cummings 1996.
Cell membranes Internal membranes
Working with Cells
117
4.2.
Basic Information
Typical Properties of Plant Cells
Domain Kingdom Nucleus Genome RNA Polymerase Starting amino acid for translation Reproduction Cellular organization Nutrition Size of cells Cell membranes After Campbell, N.A.: Biology 4/e. Benjamin/Cummings 1996.
Eukarya Plant yes linear, 107 to > 10 11 kb, organized in several chromosomes several types methionine asexual/sexual multicellular photoautotrophic average 10 100 m, wide variation rigid, contain cellulose and lignin
Internal membranes yes, they enclose organelles/vesicles
Typical Properties of Animal Cells
Domain Kingdom Nucleus Genome RNA Polymerase Starting amino acid for translation Reproduction Cellular organization Nutrition Size of cells After Campbell, N.A.: Biology 4/e. Benjamin/Cummings 1996. Cell membranes
Eukarya Animals yes linear, 107 to > 10 11 kb, organized in several chromosomes several types methionine asexual/sexual multicellular chemoheterotrophic average 10 100 m, wide variation soft, lipid bilayer only
Internal membranes yes, they enclose organelles/vesicles
Working with Cells
118
4.2.
Basic Information
Nucleic Acid and Protein content of a bacterial cell a
Per cell 950 fg 280 fg 155 fg 17 fg 100 fg 1.15 m = 1 picoliter 135 g/ml
3
Cell data Wet weight Dry weight Total Protein Total genomic DNA Total RNA Volume Intracellular protein concentration
Per liter culture (10 9 cells/ml) 950 mg 280 mg 155 mg 17 mg 100 mg
Theoretical maximum yield for a 1 liter culture (109 cells/ml) of protein of interest is 0.1% of total protein: 155 g per liter 2.0% of total protein: 3 mg per liter 50.0% of total protein: 77 mg per liter
a
values for Escherichia coli or Salmonella typhimurium
Nucleic Acid content in mammalian cells Nucleic Acid content in a typical human cell
Cell data Total DNA Total RNA Proportion of total RNA in nucleus DNA:RNA in nucleus Human genome size (haploid) Coding sequences/genomic DNA Number of genes Active genes mRNA molecules Average size of mRNA molecule Different mRNA species Per cell ~ 6 pg ~ 10 30 pg ~ 14% ~2:1 3.3 x 10 9 3% 0.5 1 x 105 1.5 x 10 4 2 x 105 1 x 10 6 1900 b 1 3 x 10 4
RNA distribution in a typical mammalian cell

RNA Species rRNA (28S, 18S, 5S) tRNAs, snRNAs mRNAs Relative amount 80 85% 15 20% 1 5%
Working with Cells
119
4.2.
Data Function
Basic Information
Nucleic Acid and Protein content in human blood*
Erythrocytes O2/CO2 transport 5 x 10 ~ 150 mg/ml (30 pg/cell)
9
Leukocytes Immune response 4 7 x 10

6
Thrombocytes Wound healing 3 4 x 108 60 80 mg/ml
Cells per ml DNA content RNA content Hemoglobin content Plasma protein content * From a healthy individual.
30 60 g/ml (6 pg/cell) 1 5 g/ml
Notes
Working with Cells
120
4.2.
Basic Information
Cell Cycle
G0 phase Interphase
resting state or dividing activity completely halted
S phase
DNA synthesis
Cytokinesis
contractile rings furrowing organelle divide
G2 phase
repair and preparator phase
growth phase
G1 phase
M phases mitosis
Prophase
chromosome condensation centriole duplication
Telophase
contractile ring formation
Prometaphase
nuclear envelope disruption
Anaphase Metaphase
spindle formation chromosomes align at equator chromosome division
Working with Cells
121
4.2.
Basic Information
Arresting Cells
Synchronization of mammalian somatic cells

Production of synchronized cells in cell cycle phase method depriviation of serum from medium L-mimosine hydroxyurea thymidine aphidicolin inhibition of protein synthesis formation of hyposunine from lysine synthesis of dNTPs DNA polymerase reversibility of block + +/+/+ suitable for fibroblasts CHO cells, HL-60 transformed human cells human fibroblasts transformed human cells transformed human cells human fibroblasts transformed human cells
G0 late G1 early S G/S
G2 M
topoisomerase II nocodazole (followed by shake-off)
toposisomerase II inhibitors depolymerization of microtubuli
+ +
Notes
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Transfection of mammalian cells
Ca2+ lipos. Transfection DNA / lipophilic agent complexes are transferred through the membrane Transduction Electroporation Microinjection Injection directly into the nucleus or cytoplasm using micro glass capillaries
Principle
Ca phosphate / DNA aggregates are transferred through the cell membrane
Reagent to be cou- A high voltage pulse pled to a transloca- is used to open the tion peptid membrane of the cells
use for DNA use for RNA use for peptides use for antibodies Cells eukaryotic cells eukaryotic cells eukaryotic cells eukaryotic cells bacteria yeasts high / low medium - high standard method for many bacteria, survival rate is critical for eukaryotic cells eukaryotic cells
Costs for equipment/ reagents Efficiency Remarks
low / low low inefficient but simple, high volumes possible
low / medium medium - high purity of DNA is important
medium low - high Trends in Cell Biology 10(2000) 290295. Nature Biotechnology 19(2001), 360364
high / medium very high non-random method, comparably few cells can be used, method of choice e.g., for antibodies
Transfection of mammalian cells (continued) General
There exist several well etablished methods for delivery of molecules, especially nucleic acids, into eukaryotic cells. However no single technique alone is suitable for the multitude of different cellular systems used for transfection experiments. Depending on the cell type and the specific experimental requirements like transfection of difficult cell lines, primary cells, easy cell lines, different molecules (DNA, RNA, oligonucleotides, proteins) or even high throughput purposes, each transfer method may possess advantages or disadvantages. Keep an eye on your cells: take care that they are in good condition and set a suitable plating protocol for optimal cell density from start to end of transfection. Dividing cells tend to be more accessible for uptake and expression of foreign DNA compared to quiescent cells. Mitogenic stimuli (e.g., virus transformation, growth factors, conditioned media, feeder cells) are often used to activate primary cells. Transfection efficiencies differ by orders of magnitude between adherent and suspension cells. It is speculated that the limiting step is the uptake by endocytosis, however, a plausible mechanistic explanation on molecular level does not exist so far. Therefore the search for more efficient transfection reagents is mainly empirical.
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Dividing vs. non-dividing cells
Adherent vs. suspension cells
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Transfection of mammalian cells (continued)
Splitting protocol
Before splitting, adherent cells have to be trypsinated in order to remove them from the substrate. This routine step means a severe obstruction of normal cellular functions. Differences in the splitting protocol (e.g., extend of trypsination, inactivation of trypsin, time untill transfection starts) could have an impact on the efficiency of transfection experiments. Cell lines tend to be unstable and therefore features may change with time in culture. The passage number indicates, how often a cell line has been splitted (normally within one lab). The exact passage number untill the line has been established is unknown in most cases. Different culture conditions could lead to clonal selection. Cell lines with the same name could therefore differ significantly with respect to physiology and morphology (and transfectability). Cell lines divide exponentially when there is space on the substrate (tissue culture dish). Growth rate is negatively affected by cell density (contact inhibition), depletion of nutrients or metabolic endproducts (e.g., pH). The extent of reporter gene expression is directly correlated with cell number at transfection start and growth rate until cell lysis.
Passage number
Cell number (grade of confluency)
DNA influences on transfection General
Control your vector: check the quality of your purified DNA and consider suitability of functional sequences for your special cellular system. Always use a control vector. Functionality of a vector depends on the structural integrity of the plasmid preparation. Supercoiled form versus relaxed form, double strand breaks, degradation by nucleases and physical stress during storage and handling influences transfection efficiency. Vectors are produced in bacterial systems and purified according to various protocols. Contaminants in the vector preparation (e.g., CsCl) may influence transfection efficiency. Often transfection systems are optimized and compared by the use of control vectors with strong viral regulatory elements (e.g., RSVa, CMVb, SV40c). However, the relative efficiacy of viral promotor/enhancer systems can differ from cell line to cell line in a range of two orders of magnitude. In some cell lines expressing the large T antigen (e.g., COS) the SV40 system is highly efficient due to autonomous plasmid amplification. In many other cell lines the CMV promotor is most efficient.
b
Vector integrity
Vector preparation
Vector architecture (Enhancer / Promoter / cDNA / poly A signal)
Respiratory Syncitial Virus
Cytomegalo Virus
Simian Virus 40
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Manipulating Cells
Transfection protocol
Establish a suitable transfection protocol: start with the standard protocol and do some tests with variations in ratio and dose for optimization. It is a common feature of all transfection reagents that DNA is packed into compact, highly condensed particles. In this form the DNA tends to be highly resistant to degradation by nucleases and inaccessible to intercalating dyes. Variables like transfection reagent/DNA-ratio, ionic strength, buffer/pH, DNA/lipid- concentrations, temperature affect the composition and the functionality of the transfection complexes. Transfection complexes are predominantly formed by charge interaction. Generally, in in vitro transfection experiments (cell lines, primary cells), complexes with a positive net-charge seem to give highest expression rates. It has often been argued that positive complexes are more efficiently adsorbed to the negatively charged cell surface. On the other hand, in in vivo approaches, complexes with an excess of negative charges proofed to be most efficient. Many transfection reagents show an optimum characteristic when the amount of transfection complex is increased. The ascending part of the curve reflects the increasing amount of DNA transfected into the cells.
Preparation of transfection complex
Transfection reagent / DNA ratio (charge ratio)
Dose dependence
The declining part of the curve reflects the cytostatic (some times cytotoxic) effect of larger amounts of transfection complex on cells. Interestingly FuGENE Transfection Reagents* does not show this decrease at the high-dose end.
Application of transfection complex
There are two alternative ways to apply the transfection complex to the cells. Either concentrated, dropwise to the medium or in combination with a medium exchange prediluted with medium. The first option is more convenient. The latter option allows a more constant application which avoids local toxic doses. The medium present during the transfection affects transfection efficiency in a positive or negative manner. This is true for different basic medium compositions and especially when calf serum has to be included. With a number of transfection reagents the efficiency is reduced in the presence of FCS (Fetal Calf Serum). Some companies provide optimized serum-free transfection media** to be used in combination with the transfection reagents. However FuGENE Transfection Reagents* are effective in the presence or absence of serum.
Transfection medium
* Available from Roche Applied Science ** Nutridoma-CS; -HU; -NS; -SP are also offered by Roche Applied Science
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Manipulating Cells
Time course of transfection
Set up a suitable time course for your transfection experiment for optimal expression of your protein of interest. 12 hours before transfection split the cells into culture plates. At the beginning of transfection the culture should be about 50% confluent, in order to nearly reach confluency at the end of the experiment. If serum is taken away during transfection cells may arrest for some time. The uptake of transfection complex by cells takes place within a period of hours (0.5h 6h). The kinetic has a saturation characteristic which means, that after a certain point no further increase in efficiency can be detected. After the application of the transfection complex, the medium has to be replaced by normal growth medium. This step is absolutely essential if transfection has to be performed in the absence of FCS. With non-toxic transfection reagents* which work in the presence of serum (e.g., FuGENE Transfection Reagents*) this step could be eliminated, if there is enough medium for the following expression period.
Start of transfection
Medium exchange
Time of analysis
Reporter gene expression is analyzed 24h to 48h after the start of transfection. Within this period, there is a constant increase in concentration of reporter gene product. It mainly depends on the sensitivity of the reporter gene assay (strength of promotor) and the lab routine when is the best time for harvesting the cells.
* Products available from Roche Applied Science, please visit and bookmark www.powerful-transfection.com
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Calcium phosphate-DNA coprecipitation
The day before transfection plate cells from exponential growth phase (1 4 x 105 cells/ml) into 12-well or 60 mm plates. One hour before the precipitate is added, the medium should be changed with fresh medium. A solution of 100 l 2.5 M CaCl2 and up to 25 g plasmid DNA is diluted with low TE buffer (1 mM Tris-HCl, 0.1 mM EDTA, pH 7.6) to a final volume of 1 ml. One volume of this 2 x Ca2+/DNA solution is added quickly to an equal volume of 2x HEPES solution (140 mM NaCl, 1.5 mM Na2HPO4, 50 mM HEPES, pH 7.05 at 23C). The cells are precipitated for 2 6 h at 37C (pH of 7.3 7.6.). After incubation, for some cell lines, e.g., CHO cells, a "glycerol shock" is advised. Cells are exposed to 20% glycerol in PBS. After 1 min the glycerol is removed by adding fresh medium, aspiration of the mixture and replacement with fresh medium. If no "glycerol shock" is used, just replace with fresh medium.
For detailed information see: Jordan M., Schallhorn A., and Wurm F.M., Transfecting mammalian cells: optimization of critical parameters affecting calcium-phosphate precipitate formation., Nucleic Acids Research, 24 (4) p.p. 596601, 1996.
Liposomal and non-liposomal Transfection Reagents

Transfection of siRNA oligos for gene knockdown applications X-tremeGENE siRNA Transfection Reagent: Proprietary blend of lipids and other components, sterile filtered and free of components derived from animals. It enables the efficient transfection of a wide range of cell lines with low cytoxic side effects and, siRNA- and cotransfection-based gene knockdown experiments. It also functions exceptionally well in the presence and absence of serum. FuGENE HD Transfection Reagent: Next-generation proprietary non-liposomal reagent that is free of animal-derived components. As proven by many scientists, it combines minimal cytotoxic side effects with excellent transfection efficiency in many cell lines not transfected well by other reagents (e.g. cell lines commonly used in oncology research, stem cells and many other difficult-to-transfect cell lines). The reagent functions in up to 100% serum and, requires a limited amount of handling steps (dilute plasmid DNA, mix with FuGENE HD Transfection Reagent, incubate and pipet the complex directly to the cells).
Transfection of plasmids and linear DNA fragments for cellular analysis, protein expression and gene knockdown applications (using shRNA expressing plasmids)
For more information and a database of successfully transfected cells, please consult www.powerful-transfection.com
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Electroporation
Electroporation uses of a transmembrane electric field pulse to induce microscopic pathways (pores) in a bio-membrane. All major manufacturers of electroporation devices offer detailed protocols for many cell lines. Electroporation is not restricted to any substance. Almost any substance that can be solved or dispersed in water can be transferred into living cells. Two very different methods are used, long Millisecond Pulses and short Microsecond Pulses. The latter are much more physiologically compatible. The cells should be in the exponential growing phase before harvesting. Adherent cells should not be more confluent than 70%. Keep treatment of adherent cells with trypsin as short as possible, otherwise the membrane gets damaged. Solve the DNA in water, or in low TE (1mM Tris-HCl, 0.1 mM EDTA, pH 7.6), EDTA inside the cell has very toxic effects. After electroporation the cell membrane is open. Handle cells with extreme care. Do no shake, aspirate very slowly with pipette.
Times and temperature are critical. Resealing of the holes in the membrane occurs during approx. 1 3 minutes at room temperature. Please note: Dont keep cells on ice because after 30 minutes the cells leak out and the ion gradient is destroyed.
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Electroporation
Calculating the Required Field Strength for Electroporation
A standard value for the required field strength can be calculated using the following formula: Vc Ec = 1.5 x a Example: Cell radius a = 10 m = 10 106 cm Critical breakdown voltage at room temperature Vc = 1 V [Vc (4C) = 2 V] Critical field strength Ec = 1V 1.5 x 10 x 10 cm
-4
= 666
V cm
The voltage required for the Multiporator can be calculated using the field strength which has been calculated and the distance between the electrodes in the cuvette (d: Distance between electrodes [cm]): V = Ec d Example for 2 mm cuvettes: 666
Suggestion for a test series:
cm cm 1. Voltage applied: 130 V 2. Voltage applied: 160 V 3. Voltage applied: 200 V 4. Additional voltage 240 V and in appropriate increments
x 0.2 cm = 133
Voltage Profile
1000 800 Voltage [Volt] 600 400 200 0
= 30 s
Time [s]
Voltage Profile of Eppendorf Multiporator in Mammalian Transfection Mode
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Microinjection
This physical method offers the best possible transfection efficiency as the DNA is brought directly into the cell nucleus. Cells are injected using an extremely fine glass capillary (e.g., Eppendorf Femtotips) which is filled with DNA, RNA or any other liquid reagent. With the aid of a micromanipulator (e.g., Eppendorf InjectMan 5179) this glass capillary is moved into the cells and with the aid of a microinjector (e.g., Eppendorf FemtoJet 5247) pressure is applied to force the liquid into the cells. Microinjection is the only non-random transfection method available. It has some unique advantages and limitations as well.
Advantages 1. It is the only method where the user can actively decide which cells should be transfected. 2. It is possible to inject directly into the nucleus or the cytoplasm of a cell. 3. Cells remain in their cellular context; thus, intra- and extracellular signals or transport processes can be analyzed. 4. Co-transfection of different reagents is possible. 5. The cells can be monitored in real time during the transfection process. 6. In principle any kind of cells or substances can be used for microinjection. Limitations 1. The number of cells that can be analyzed is limited. Using automatic microinjectors, a maximum of about 1000 adherent cells per hour can be transfected. If suspension cells are used this number is even much lower. 2. The equipment is rather expensive. 3. It takes time to be an expert with this technique.
Use of Selection Markers for Stable Cell Lines
Seed cells at 25% confluence, let the cells grow overnight. Substitute the cells with medium containing varying concentration of selection reagent Replace the selection medium every 3 to 4 days Determine the appropiate concentration of selection reagent
Selection Reagent Blasticidin G-418 (Neomycin) Hygromycin* Zeocin Concentration 1 to 20 g/ml 50 to 1000 g/ml 10 to 500 g/ml 50 to 1000 g/ml Cell death after 7 to 10 days 7 to 14 days 7 to 14 days 7 to 14 days
* Product available from Roche Applied Science
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Apoptosis/Necrosis
Terminology of cell death
Cell death can occur by either of two distinct6,7 mechanisms: Necrosis or Apoptosis. In addition, certain chemical compounds and cells are said to be cytotoxic to the cell, that is, to cause its death. Someone new to the field might ask, what's the difference between these terms? To clear up any possible confusion, we start with some basic definitions. The two mechanisms of cell death may briefly be defined: Necrosis ("accidental" cell death) is the pathological process which occurs when cells are exposed to a serious physical or chemical insult. Apoptosis ("normal" or "programmed" cell death) is the physiological process by which unwanted or useless cells are eliminated during development and other normal biological processes. Cytotoxicity is the cell-killing property of a chemical compound (such as a food, cosmetic, or pharmaceutical) or a mediator cell (cytotoxic T cell). In contrast to necrosis and apoptosis, the term cytotoxicity does not indicate a specific cellular death mechanism. For example, cell-mediated cytotoxicity (that is, cell death mediated by either cytotoxic T lymphocytes [CTL] or natural killer [NK] cells) combines some aspects of both necrosis and apoptosis.
Necrosis and apoptosis
Cytotoxicity
Illustration of the morphological features of necrosis and apoptosis
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Apoptosis/Necrosis
Differences between necrosis and apoptosis
There are many observable morphological and biochemical differences between necrosis and apoptosis. Necrosis occurs when cells are exposed to extreme variance from physiological conditions (e.g., hypothermia, hypoxia) which may result in damage to the plasma membrane. Under physiological conditions direct damage to the plasma membrane is evoked by agents like complement and lytic viruses. Necrosis begins with an impairment of the cell's ability to maintain homeostasis, leading to an influx of water and extracellular ions. Intracellular organelles, most notably the mitochondria, and the entire cell swell and rupture (cell lysis). Due to the ultimate breakdown of the plasma membrane, the cytoplasmic contents including lysosomal enzymes are released into the extracellular fluid. Therefore, in vivo, necrotic cell death is often associated with extensive damage resulting in an intense inflammatory response. Apoptosis, in contrast, is a mode of cell death that occurs under normal physiological conditions and the cell is an active participant in its own demise ("cellular suicide").
It is most often found during normal cell turnover and tissue homeo stasis, embryogenesis, induction and maintenance of immune tolerance, developement of the nervous system and endocryne-dependent tissue atrophy. Cells undergoing apoptosis show characteristic morphological and biochemical features. These features include chromatin aggregation, nuclear and cytoplasmic condensation, partition of cytoplasm and nucleus into membrane bound-vesicles (apoptotic bodies) which contain ribosomes, morphologically intact mitochondria and nuclear material. In vivo, these apoptotic bodies are rapidly recognized and phagocytized by either macrophages or adjacent epithelial cells. Due to this efficient mechanism for the removal of apoptotic cells in vivo no inflammatory response is elicited. In vitro, the apoptotic bodies as well as the remaining cell fragments ultimately swell and finally lyse. This terminal phase of in vitro cell death has been termed secondary necrosis.
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Apoptosis/Necrosis
Necrosis Apoptosis Membrane blebbing, but no loss of integrity Aggregation of chromatin at the nuclear membrane Begins with shrinking of cytoplasm and condensation of nucleus Ends with fragmentation of cell into smaller bodies Formation of membrane bound vesicles (apoptotic bodies) Mitochondria become leaky due to pore formation involving proteins of the bcl-2 family. Affects individual cells Inducted by physiological stimuli (lack of growth factors, changes in hormonal environment) Phagocytosis by adjacent cells or macrophages No inflammatory response
Morphological features
Loss of membrane integrity Begins with swelling of cytoplasm and mitochondria Ends with total cell lysis No vesicle formation, complete lysis Disintegration (swelling) of organelles
Physiological significance
Affects groups of contiguous cells Evoked by non-physiological disturbances (complement attack, lytic viruses, hypothermia, hypoxia, ischemic, metabolic poisons) Phagocytosis by macrophages Significant inflammatory response
Biochemical features
Loss of regulation of ion homeostasis No energy requirement (passive process, also occurs at 4C) Random digestion of DNA (smear of DNA after agarose gel electrophoresis Postlytic DNA fragmentation (= late event of death)
Tightly regulated process involving activation and enzymatic steps Energy (ATP)-dependent (active process, does not occur at 4C) Non-random mono- and oligo nucleosomal length fragmentation of DNA (Ladder pattern after agarose gel eletrophoresis) Prelytic DNA fragmentation Release of various factors (cytochrome C, AIF) into cytoplasm by mitochondria Activation of caspase cascade Alternations in membrane asymmetry (i.e., translocation of phosphatidylserine from the cytoplasmic to the extracellular side of the membrane)
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Apoptosis Assay Methods
Originally, to study both forms of cell death, necrosis and apoptosis, cytotoxicity assays were used. These assays were principally of two types: Radioactive and non-radioactive assays that measure increases in plasma membrane permeability, since dying cells become leaky. Colorimetric assays that measure reduction in the metabolic activity of mitochondria, mitochondria in dead cells cannot metabolize dyes, while mitochondria in living cells can. However, as more information on apoptosis became available, that both types of cytotoxicity assays vastly underestimated the extent and timing of apoptosis. For instance, early phases of apoptosis do not affect membrane permeability, nor do they alter mitochondrial activity. Although the cytotoxicity assays might be suitable for detecting the later stages of apoptosis, other assays were needed to detect the early events of apoptosis. In relation with increased understanding of the physiological events that occour during apoptosis, a number of new assay methods have been developed. For instance, these assays can measure one of the following apoptotic parameters:
Fragmentation of DNA in populations of cells or in individual cells, in which apoptotic DNA breaks into different fragments. Alternations in membrane asymmetry. Phosphatidylserine translocates from the cytoplasmic to the extracellular side of the cell membrane. Activation of apoptotic caspases. This family of protease sets off a cascade of events that disable a multitude of cellular functions. Release of cytochrome C and AIF into cytoplasma by mitochondria.
For more details please check out http://www.roche-applied-science.com/apoptosis
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Analyzing Cells
Apoptosis Assay Methods: Selection Guide
All Products are available from Roche Applied Science, http://www.roche-applied-science.com/apoptosis
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General
Analyzing Cells
Cell Proliferation and Viability
Rapid and accurate assessment of viable cell number and cell proliferation is an important requirement in many experimental situations involving in vitro and in vivo studies. Usually, one of two parameters are used to measure the health of cells Can be defined as the number of healthy cells in a sample. Whether the cells are actively dividing or are quiescent is not distinguished. Cell viability assays are often useful when non-dividing cells (such as primary cells) are isolated and maintained in culture to determine optimal culture conditions for cell populations. Methods for determining viable cell number is a direct counting of the cells in a hemocytometer, cell morphology (staining), metabolic activity Is the measurement of the number of cells that are dividing in a culture. Methods for determination: clonogenic assays (plate cells on matrix), establish growth curves (time-consuming), measurement of DNA synthesis (3H-thymidine or bromodeoxyuridine), indirect parameters (measure cell cycle regulating molecules)
Cell Viability
Cell Proliferation
Notes
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Proliferation Assay Methods: Selection Guide
All Products are available from Roche Applied Science, http://www.roche-applied-science.com/apoptosis
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General
Analyzing Cells
FACS (Fluorescence activated cell sorting)
powerful technique used in flow cytometry to physically separate and identify specific types of cells from heterogeneous populations.
Procedure: Staining of surface proteins on intact cells

Sensitivity: +++ Duration: + Sensitivity: ++ Duration: ++ Sensitivity: + Duration: +++
Biotin-Streptavidin enhancement
Directly labeled 2nd Ab
Directly labeled primary antibody
Harvest Cells (5x105) per stain, (For suspending adherent cells, try EDTA (2mM in PBS, incubate at 37C) first. Trypsin solutions might damage surface antigens and preclude their detection) Wash cells once with FACS buffer Incubate with first antibody 30 min (110 g/ml) Wash cells with FACS buffer Add Biotinylated 2nd Ab (110 g/ml) Wash cells with FACS buffer Add streptavidin linked fluorochrome (15 g/ml) incubate 1530 min. Wash, resuspend in FACS buffer, measure All incubations should be done on ice. Keep solutions in the dark after addition of the fluorochrome. Add labeled 2nd Antibody, incubate 30 min. Incubate with directly labeled antibody.
For discrimination of dead cells, Propidium Iodide (PI) or 7-Aminoactinomycin-D (7-AAD) can be added in the final step. Propidium Iodide (PI) and 7-Aminoactinomycin-D (7-AAD) selectively enter dead cells and lead to high fluorescence in FL3 allowing to exclude them from analysis (dead cells may bind antibodies unspecifically). Controls
Control type Cells only in FACS-Buffer Parameter controlled Autofluorescence, used for setting up Instrument Influenced by Cell Type, Cell treatment (some chemicals exhibit strong autofluorescence!). Dead cells might exhibit stronger autofluorescence. Immunoglobulin receptors on the cell surface (might bind secondary antibody). Secondary reagents might stick to dead (permeabilized) cells.
Omit first antibody (not for directly labelled) Controls non-specific binding of secondary reagents. Isotype control antibody instead of primary antibody. Controls specificity of staining for primary antibody
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FACS
Measurements
Name FSC (Forward Scatter) SSC (Sideward scatter) FL 14 (Fluorescence channel 14) Measured parameter Size of cell Granularity of cell Detection of antibodies, fluorescent proteins (eg. GFP), and DNA binding molecules
1: Switch on FACS, check levels of sheath, waste etc. (ask operator) 2: With the unstained cells as sample, set up the following Set up dot plot view of FSC vs. SSC adjust amplification levels so that bulk of cells is in window. Set gate on population to be measured (Fig. 1) Set up histogram view of fluorescence channel(s) to be measured. Adjust fluorescence level of channel(s) to be used, so that the bulk of the cells is in the first decade (Fig. 2)
Fig 1
Fig 2
Fig 1: FSC vs. SSC plot. Intact cells are located in the gate R1 (red). Dead cells and debris are in the gate R2 (green). Fig 2: Overlay of measurements of population R1 from Fig.1. Black: Autofluorescence. Blue: Isotype control antibody. Red: Specific antibody.
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FACS
Troubleshooting
No signal/no cells visible in FSC/SSC plot: Cells lost during staining? Check with a microscope. FSC/SSC amplification too high or low (cells are not in the window)? Try lowering/raising the amplification. Problem with the FACS system. Restart the system. No clear population, cells are spread in FSC SSC plot Air bubbles are aspirated ? Refill flow path with buffer (Prime) Cells lost? Check with microscope. Stainings can be conveniently done in 96 well round-bottom plates, for easy handling with a multichannel pipettor. Small samples (50 200 l) can be measured in (H3) tubes. Just put one of the small tubes in a larger 'Facs' tube. For measurement of small samples the outer needle jacket should be removed to prevent complete sample aspiration.
Tips
Notes
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Analyzing Cells
Overview: Reporter Gene Assays
CHEMILUMINESCENCE Sensitivity Time (h) Material ELISA Histology WESTERN BLOT
Chemical
CAT
non endogeneous activity bio- and chemical assays
narrow linear range endogeneous activity (mammalian cells) requires substrate + O2 + ATP
10 pg
E*
Immunological 1 ng/band 1 ng/band
-Gal
20 fg
E*
1.5 2.5
10 pg
E*
Luc
high specific activity
5 fg 1 pg
E*
0.5
Time (h) 4
Material
REPORTER
Sensitivity
* E = Extract
hGH*
secreted protein
cell lines with defects in the secretary pathway endogeneous activity in some cells & cell lines with defects in the secretary pathway requires posttranslational modifications
1 pg
S*
1 ng/ band
SEAP
secreted protein
10 fg
S*
1 ng/ band
GFP
auto-fluorescence
5 ng/ band
* no cross-reactivity with rat GH ** S = Supernatant
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Reporter systems contribute to the study of eukaryotic gene expression and regulation by joining a promoter sequence to an early detectable reporter gene. Reporter systems are also used to check transfection efficiency. CAT* -Gal* Luc* hGH* SEAP* GFP Chloramphenicol Acetyltransferase -Galactosidase Luciferase Human Growth Hormon Secreted Human Placental Alkaline Phosphatase Green Fluorescent Protein
* Nonradioactive Reporter Gene Assays available from Roche Applied Science; please visit: http://www.roche-applied-science.com
Notes
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Analyzing Cells
Method/detection Advantages Produces a high intensity light emission (t1/2 5 min) Optimized lysis buffer for dual reporter genes assays Dynamic range/Sensitivity
Luciferase Reporter Gene Assay high sensitivity Luciferase Reporter Gene Assay constant light signal
Luciferase Reporter Gene Assay, high sensitivity
Quantify enzymatically active luciferase D-Luciferin/ chemiluminescence
Luciferase Reporter Gene Assay, constant light signal
Quantify enzymatically active luciferase Luciferin/chemiluminescence
Produces an extended light emission (t1/2 3h) Ideal for high throughput screening (HTS) Optimized lysis buffer for dual reporter genes Sensitivity comparison of Luciferase Reporter Gene Assays
hGH ELISA (secreted human growth hormone)
ELISA for hGH secreted in culture medium Measure total (active and inactive) hGH Colorimetric, fluorescent, or chemiluminescent detection
20 times more sensitive than 5 ng400 ng/ml of cell extract isotopic hGH assays No cell lysis required Study protein expression kinetics over extended periods Master-lot standardization*
Method/detection -Gal Reporter Gene Assay, chemiluminescent Quantify enzymatically active -Gal Galacton PlusTM Chemiluminescent Substrate
Advantages Highly sensitive Measures only active enzyme Extended light emission (t1/2 10 min) Optimized lysis buffer for dual reporter genes Nonradioactive assay Master-lot standardization* Specific for bacterial -glactosidase Optimized lysis buffer for dual reporter genes Easy to use. Mix reagents and apply to cells or tissue section No cell lysis required Extended light emission (t1/2 1h) Assay culture medium for reporter protein Study protein expression kinetics
Dynamic range/Sensitivity 400 pg400 pg/ml of cell extract
-Gal ELISA
ELISA determines total expressed (active and inactive) -Gal enzyme Colorimetric, fluorescent, or chemiluminescent detection Measures enzymatic activity Histochemical stain for -Gal expressing cells ortissue sections Quantify enzymatically active alkaline phosphatase in culture medium CSPD Chemiluminescent Substrate
50 pg1000 pg/ml of cell extract
-Gal Staining Set
SEAP Reporter Gene Assay, chemiluminescent (secreted alkaline phosphatase)
500 fg50 ng/ ml of of cell extract
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Method/detection Advantages Highly sensitive Master-lot standardization* Anti-CAT-coated tubes and micro-titer plates available for detection Optimized lysis buffer for dual reporter genes Easy to use. Mix reagents and apply to cells or tissue section Dynamic range/Sensitivity 200 pg1000 pg/ml of cell extract
CAT
ELISA determines total expressed (active and inactive) CAT enzyme Colorimetric, fluorescent, or chemiluminescent detection
CAT Staining Set
Measures enzymatic activity Histochemical stain for CAT expressing cells or tissue sections
CAT ELISA performed with various detection systems * Master-lot standardized controls and the provided lot specific information enables direct comparison of data from different sets of experiments, even when kits from different production lots are used. As a result, you can compare results from assays run at different times. All reporter gene assays listed are available from Roche Applied Science.
4.5.
1. 2. 3. 4. 5. 6. 7. 8. 9.
References
Schwartzman, R. A. and Cidlowski, J. A. (1993) Apoptosis: the biochemistry and molecular biology of programmed cell death. Endocrine Rev. 14, 133 Vermes, I. and Haanan, C. (1994) Apoptosis and programmed cell death in health and disease. Adv. Clin. Chem. 31, 177 Application Manual: Apoptosis, Cell Death and Cell Proliferation, 3rd edition (2004), Roche Applied Science Transfection Reagents and Reporter Gene Assays, (2002) Roche Applied Science Brochure: Protein Expression and Analysis (2005), Roche Applied Science D. Kahle and K. Lukas, personal communication, Eppendorf GmbH Brochure: The cpmplete Guide for Protease Inhibition (2006), Roche Applied Science Brochure: Gene Knockdown: Integrated solutions for effective and specific gene knockdown (2005), Roche Applied Science Brochure: FuGENE HD Transfection Reagent: Cover new ground - one reagent for superior results" (2007), Roche Applied Science
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Preparing Buffers and Media

Chapter 5
5.1. 5.2. 5.3. 5.4.
Buffers ................................................................................. Antibiotics ........................................................................... Media for Bacteria .......................................................... References .........................................................................
146 160 161 163
5.1.
Term Mole
Buffers
Definitions
Symbol mol Meaning An amount containing Avogadros* number of whatever units are being considered. Avogadros* number = 6.023 x 1023 Concentration of a substance in a liquid. moles of substance Molarity = liter of solution Example 1 mol H2O molecules = 6.023 x 1023 H2O molecules.
Molar or Molarity
mol/liter or M
An 1 M (mol/liter) solution of Tris in H2O is prepared by dissolving 1 mol Tris molecules in H2O to a final volume of 1 liter.
Molar weight
g/mol
Weight of 1 mol (= 6. 023 x 1023 parts) of a molecule, Molecular weight of Tris: 121.1 g/mol. An 1 M (mol/ as defined by the molecular weight of this molecule. liter) solution of Tris in H2O is prepared by dissolving 121.1 g Tris in H2O to a final volume of 1 liter.
Example: How many grams of NaOH are needed to make up a 100 ml solution of 5 M NaOH (= 5 mol/l)? Formula: Needed grams = Concentration x Molecular weight x Final volume = 5 mol/liter x 40 g/mol x 0.1 liter = 20 g
* Named after Amedeo Avogadro (1776 1856), a famous Italian physical chemist.
Precautions Reagents H2O
Use the highest possible purity grade of reagents. Prepare all solutions with fresh double-distilled or deionized H2O. Only use H2O from a destillation or deionization unit with a resistance value of 18 MOhm/cm. Regularly clean the units following instructions from the manufacturers. Remove reagents from parent vials by shaking, do not use spatulas. Wear gloves. Take the water of crystallization into account when calculating the amount of reagent needed to make solutions with a given molarity. e.g., Molecular weight of MgSO 4 7H2O = 120.37 (MW of MgSO4) + 126.11 (MW of 7 molecules H2O) = 246.48 By autoclaving: 0.5 liter solution: ~ 15 minutes at 121C at 1 bar 1 liter solution: ~ 20 minutes at 121C at 1 bar Caution: certain buffers (e.g., containing glucose, SDS, -mercaptoethanol) should not be autoclaved. Use filtration through an 0.22 m filter as an alternative.
Preparing Buffers
Sterilizing
146
5.1.
Buffers
Precautions (continued)
pH measurement
Always fix the pH electrode in a vertical position. Gently stir the solution when adjusting the pH. Never put the electrode in solutions containing SDS. Periodically calibrate the electrode with at least two calibration solutions. Store the pH electrode in solution, keep the diaphragm wet and make sure that there is always electrolyte solution inside the electrode. Clean the pH electrode with distilled water after usage. Caution: the pH of most solutions is temperature-dependent: e.g.,: 5C: pH of a 0.05 M Tris solution = 8.07 25C: pH of a 0.05 M Tris solution = 7.50 37C: pH of a 0.05 M Tris solution = 7.22 Carefully consult the product safety information and material safety data sheets of chemicals. Take local safety and laboratory regulations into account when working with chemicals.
Safety
Notes
147
5.1.
pH 5.5
Buffers
Buffering ranges of commonly used buffers (at 20C)
6 MES ADA ACES PIPES MOPSO BES MOPS TES HEPES TRIS EPPS TRICINE BICINE TAPS GLYGLY CHES CAPS 6.5 7 7.5 8 8.5 9 9.5 10 10.5 11 11.5 6.1 6.6 6.8 6.8 6.9 7.1 7.2 7.4 7.5 8.1 8.0 8.1 8.3 8.4 8.4 9.3 10.4 pKa
Recipes for stock solutions 10 M NH4OAc 1 liter
Dissolve 770.8 g ammonium acetate (NH4OAc, MW = 77.08) in 800 ml H2O. Adjust volume to 1 liter with H2O. Sterilize by autoclaving and store at room temperature. Dissolve 219.08 g calcium chloride 6H2O (CaCl2 6H2O, MW = 219.08) in 800 ml H2O. Adjust volume to 1 liter with H2O. Sterilize by autoclaving and store at room temperature. Dissolve 50 g Ficoll 400, 50 g polyvinylpyrrolidone and 50 g bovine serum albumin (BSA*) in 600 ml H2O. Adjust volume to 1 liter with H2O. Divide in aliquots of 25 ml and store at 20C. Dissolve 3.085 g 1,4-dithio-DL-threitol (DTT, MW = 154.25) in 20 ml 10 mM sodium acetate (pH 5.2). Divide in aliquots of 1 ml and sterilize by filtration. Store at 20C.
1 M CaCl2 1 liter
250 x Denhardt Solution 1 liter
1 M DTT* 20 ml
148
5.1.
Buffers
Recipes for stock solutions (continued)
0.5 M Na2EDTA (pH 8.0) 1 liter
Dissolve 186.12 g disodium ethylenediaminetetraacetate 2H2O (Na2 EDTA 2H2O, MW = 372.24) ) in 800 ml H2O; stir vigorously on a magnetic stirrer. Adjust to pH 8.0 with NaOH (~ 20 g NaOH pellets) and adjust volume to 1 liter with H2O. Divide into aliquots and sterilize by autoclaving. Store at room temperature. Note: the disodium salt of EDTA will only solute when the pH of the solution is adjusted to 8.0 by the addition of NaOH. Dissolve 1.19 g isopropyl -D-thiogalactopyranoside (IPTG, MW = 238.3) in 40 ml H2O. Adjust volume to 50 ml with H2O. Divide in 5 ml aliquots and sterilize by filtration. Store at 20C, this solution is stable for 2 4 months. Dissolve 203.31 g magnesium chloride 6H2O (MgCl2 6H2O, MW = 203.31) in 800 ml H2O. Adjust volume to 1 liter with H2O. Divide in aliquots of 100 ml and sterilize by autoclaving. Store at room temperature.
0.1 M IPTG* 50 ml
1 M MgCl2* 1 liter
10 x MOPS* 1 liter
Add 41.85 g 4-morpholinopropanesulfonic acid (MOPS free acid, MW = 209.27) and 6.80 g sodium acetate 3H2O (NaOAc 3H2O, MW = 136.08) to 800 ml DEPC treated H2O and stir until completely dissolved. Add 20 ml of a DEPC treated 0.5 M Na2EDTA solution and adjust pH to 7.0 with 10 M NaOH. Adjust volume to 1 liter with DEPC treated H2O. Divide into 200 ml aliquots and store protected from light at 4C. If the solution turns yellow, use a new aliquot. Dissolve 408.24 g sodium acetate 3H2O (NaOAc 3H2O, MW = 136.08) in 800 ml H2O. Adjust to pH 5.2 with glacial acetic acid or to pH 7.0 with diluted acetic acid. Adjust volume to 1 liter with H2O. Sterilize by autoclaving and store at room temperature. Dissolve 292.2 g sodium chloride (NaCl, MW = 58.44) in 800 ml H2O. Adjust volume to 1 liter with H2O. Sterilize by autoclaving and store at room temperature.
3 M NaOAc 1 liter
5 M NaCl 1 liter
149
5.1.
Buffers
Recipes for stock solutions (continued)
10% SDS* 1 liter
Dissolve 100 g sodium dodecyl sulfate crystals (SDS) in 900 ml H2O. Heat to 68C to solute the crystals. Adjust pH to 7.2 with HCl (~ 50 l). Adjust volume to 1 liter with H2O. Dispense into aliquots and store at room temperature. Note: the fine crystals of SDS disperse easily, wear a mask when weighing SDS and clean the weighing area and balance after use. When SDS crystals precipitate (e.g., due to cold temperature), redissolve by warming the solution at 37C. Add 500 g trichloroacetic acid (TCA) to 227 ml H2O. This solution contains 100% (w/v) TCA. Dissolve 121.14 g tris(hydroxymethyl)aminomethane (Tris, MW = 121.14) in 800 ml H2O. Adjust pH to the desired value by adding concentrated HCl: pH 7.4: ~ 70 ml pH 7.6: ~ 60 ml pH 8.0: ~ 42 ml Adjust volume to 1 liter with H2O. Sterilize by autoclaving and store at room temperature.
100% (w/v) TCA 1 M Tris* 1 liter
X-gal* (20 mg/ml) 20 ml
Dissolve 400 mg 5-Bromo-4-Chloro-3-Indolyl--D-galactoside (X-gal) in 20 ml N,N-dimethyl formamide. Divide into 500 l aliquots and store in a glass or polypropylene tube protected from light at 20C. This stock solution is stable for 2 4 months.
150
5.1.
Buffers
Recipes for buffers
10 x PBS* 1 liter
Dissolve 80 g NaCl, 2 g KCl, 26.8 g Na2HPO4 7H2O and 2.4 g KH2PO4 in 800 ml H2O. Adjust to pH 7.4 with HCl. Adjust volume to 1 liter with H2O. Divide in aliquots and sterilize by autoclaving. Store at room temperature. Dissolve 175.3 g NaCl and 88.2 g sodium citrate 2H2O in 800 ml H2O. Adjust pH to 7.0 with HCl. Adjust volume to 1 liter with H2O. Divide in aliquots and sterilize by autoclaving. Store at room temperature. Dissolve 175.3 g NaCl, 27.6 g NaH2PO4 1H2O and 7.4 g Na2EDTA in 800 ml H2O. Adjust pH to 7.4 with NaOH (~ 6.5 ml of a 10 M solution). Adjust volume to 1 liter with H2O. Divide in aliquots and sterilize by autoclaving. Store at room temperature.
20 x SSC* 1 liter
20 x SSPE 1 liter
1 x TE 1 liter
Add 10 ml 1 M Tris (pH 8.0, 7.6 or 7.4) and 2 ml 0.5 M Na2EDTA** (pH 8.0) to 800 ml H2O. Mix and adjust volume to 1 liter with H2O. Sterilize by autoclaving. Store at room temperature.
* Products available from Roche Applied Science ** For certain applications (e.g., storage of DNA that will be used in PCR or other enzymatic reactions), add 200 l 0.5 M Na2EDTA instead of 2 ml.
151
5.1.
Buffers
Recipes for buffers with desired pH 0.2 M acetic acid:
0.1 M NaOAc 100 ml
mix 11.55 ml glacial acetic acid in 500 ml H2O and adjust to 1 liter with H2O.
0.2 M sodium acetate:
dissolve 27.21 g sodium acetate 3H2O (NaOAc 3H2O, MW = 136.08) in 800 ml H2O and adjust to 1 liter with H2O. The table below gives the volumes in ml of these solutions and H2O that should be mixed to obtain a 100 ml solution of 0.1 M NaOAc with a specific desired pH.
0.1 M KOAc 100 ml 0.2 M acetic acid:
mix 11.55 ml glacial acetic acid in 500 ml H2O and adjust to 1 liter with H2O
0.2 M potassium acetate:
dissolve 19.62 g potassium acetate (KOAc, MW = 98.14) in 800 ml H2O and adjust to 1 liter with H2O. The table below gives the volumes in ml of these solutions and H2O that should be mixed to obtain a 100 ml solution of 0.1 M KOAc with a specific desired pH.
pH table for acetate buffersa
Desired pHa 3.6 3.8 4.0 4.2 4.4 4.6 4.8 5.0 5.2 5.4 5.6
a
0.2 M acetic acid solution (ml) 46.3 44.0 41.0 36.8 30.5 25.5 20.0 14.8 10.5 8.8 4.8
0.2 M sodium or potassium acetate solution (ml) 3.7 6.0 9.0 13.2 19.5 24.5 30.0 35.2 39.5 41.2 45.2
H2O (ml) 50 50 50 50 50 50 50 50 50 50 50
It is strongly recommended to check the final pH with a pH meter.
152
5.1.
Buffers
Recipes for buffers with desired pH (continued) 0.2 M sodium phosphate, mono-sodium salt:
0.1 M Na Phosphate 200 ml
dissolve 27.6 g NaH2PO4 1H2O (MW = 138) in 500 ml H2O and adjust to 1 liter with H2O
0.2 M sodium phosphate, di-sodium salt:
dissolve 53.62 g Na2HPO4 7H2O (MW = 268.1) in 500 ml H2O and adjust to 1 liter with H2O. The table below gives the volumes in ml of these solutions and H2O that should be mixed together to obtain a 200 ml solution of 0.1 M Na-phosphate with a specific desired pH.
0.1 M K Phosphate 200 ml 0.2 M potassium phosphate, mono-potassium salt:
dissolve 27.2 g KH2PO4 (MW = 136.09) in 500 ml H2O and adjust to 1 liter with H2O
0.2 M potassium phosphate, di-potassium salt:
dissolve 34.8 g K2HPO4 (MW = 174.18) in 500 ml H2O and adjust to 1 liter with H2O. The table below gives the volumes in ml of these solutions and H2O that should be mixed together to obtain a 200 ml solution of 0.1 M K-phosphate with a specific desired pH.
pH table for phosphate buffersa:

sodium or potassium, sodium or potassium, Desired phosphate mono salt phosphate di salt a pH solution (ml) solution (ml) 5.7 5.8 5.9 6.0 6.1 6.2 6.3 6.4 6.5 6.6 6.7 6.8
a It
H2O (ml) 100 100 100 100 100 100 100 100 100 100 100 100
sodium or potassium, sodium or potassium, Desired phosphate mono salt phosphate di salt a pH solution (ml) solution (ml) 6.9 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 7.9 8.0 45.0 39.0 33.0 28.0 23.0 19.0 16.0 13.0 10.5 8.5 7.0 5.3 55.0 61.0 67.0 72.0 77.0 81.0 84.0 87.0 90.5 91.5 93.0 94.7
H2O (ml) 100 100 100 100 100 100 100 100 100 100 100 100
93.5 92.0 90.0 87.7 85.0 81.5 77.5 73.5 68.5 62.5 56.5 51.0
6.5 8.0 10.0 12.3 15.0 18.5 22.5 26.5 31.5 37.5 43.5 49.0
is strongly recommended to check the final pH with a pH meter.
153
5.1.
Buffers
Recipes for buffers with desired pH (continued)
0.05 M Tris 100 ml
The table below gives the volumes of 0.1 M Tris buffer, 0.1 M HCl and H2O that should be mixed together to obtain a 100 ml solution of 0.05 M Tris with a specific desired pHa :
Desired pHa 7.3 7.4 7.5 7.6 7.7 7.8 7.9 8.0 8.1 8.2 8.3 8.4 8.5 8.6
a
pH table for Tris buffers
0.1 M HCl (ml) 43.4 42.0 40.3 38.5 36.6 34.5 32.0 29.2 26.2 22.9 19.9 17.2 14.7 12.4
0.1 M Tris (ml) 50 50 50 50 50 50 50 50 50 50 50 50 50 50
H2O (ml) 6.6 8.0 9.7 11.5 13.4 15.5 18.0 20.8 23.8 27.1 30.1 32.8 35.3 37.6
It is strongly recommended to check the final pH with a pH meter.
Electrophoresis of DNA 10 x agarose gel sample buffer 100 ml 10 x TBE* (Tris-borate) 1 liter 50 x TAE* (Tris-acetate) 1 liter 10 x TPE (Tris-phosphate) 1 liter
Dissolve 250 mg bromophenol blue and/or 250 mg xylene cyanol in 33 ml 150 mM Tris pH 7.6. Add 60 ml glycerol and 7 ml H2O. Store at room temperature. Dissolve 108 g Tris and 55 g Boric acid in 900 ml H2O. Add 40 ml 0.5 M Na2EDTA (pH 8.0) and adjust volume to 1 liter with H2O. Store at room temperature. Dissolve 242 g Tris in 500 ml H2O. Add 100 ml 0.5 M Na2EDTA (pH 8.0) and 57.1 ml glacial acetic acid . Adjust volume to 1 liter with H2O. Store at room temperature. Dissolve 108 g Tris in 700 ml H2O Add 15.5 ml 85% Phosphoric acid (1.679 g/ml) and 40 ml 0.5 M Na2EDTA (pH 8.0). Adjust volume to 1 liter with H2O Store at room temperature
* Products available from Roche Applied Science as convenient ready-to-use solutions
154
5.1.
Buffers
Electrophoresis of RNA
RNA Sample buffer
Mix 10 ml deionized formamide, 3.5 ml 37% formaldehyde and 2 ml 5 x MOPS. Divide into 500 l aliquots and store at 20C. The buffer is stable for 6 months. Use 2 parts sample buffer for each part of RNA. Note: Formamide is a teratigen and formaldehyde is a carcinogen. Work in a fumehood and follow laboratory safety procedures. Prepare in DEPC-treated H2O: 50% glycerol, 1 mM Na2EDTA, and 0.4% Bromophenol Blue. Use the highest possible grade of glycerol to avoid ribonuclease contamination. Divide into 500 l aliquots and store at 20C. Use 2 l loading buffer per 10 20 l RNA sample (RNA plus sample buffer).
RNA Loading Buffer
DEPC-treatment DEPC-treatment per 100 ml solution
Add 0.1 0.2 ml diethylpyrocarbonate (DEPC) to 100 ml of a solution (e.g., H2O). Shake vigorously and incubate overnight in a fume hood. Autoclave the solution to inactivate the remaining DEPC. Store treated solution at room temperature. Note: Wear gloves and use a fume hood when using DEPC (suspected carcinogen). All chemical substances containing amino groups (e.g., Tris, MOPS, EDTA, HEPES, etc.) cannot be treated directly with DEPC. Prepare these solutions in DEPC-treated H2O.
155
5.1.
Buffers
Staining of Nucleic Acids
Ethidium Bromide 100 ml
Prepare a stock solution of 10 mg/ml by adding 1 g ethidium bromide to 100 ml H2O. Stir until the dye has complete dissolved. Store in the dark at 4C. Staining: During electrophoresis: add 0.5 1 g per ml agarose solution After electrophoresis: add 0.5 2 g per ml staining solution Caution: Ethidium bromide is a mutagen and is toxic. Wear gloves when working with the solution and wear a mask when dissolving the powder. Supplied* as a stock solution in DMSO, stable at 20C for 6 12 months. Working solution: dilute the stock solution 1:10,000 in TE, TBE or TAE buffer. Sensitivity: as low as 80 pg per band dsDNA using 312 nm transillumination with the Lumi-Imager F1 System. Dissolve 500 g phenol in 500 ml 1 M Tris (pH 8.0). Once dissolved, let phases separate and remove upper aqueous phase. Add 500 ml 100 mM Tris (pH 8.0); stir to emulsify and let phases separate.
SYBR Green I Nucleic Acid Gel Stain*
Phenol* 1 liter
Repeat procedure with TE until pH of upper, aqueous phase is less than pH 7.2. Store at 4C protected from light. Discard when the solution turns red/brown.
Phenol* (acid) 1 liter For RNA only!
Dissolve 500 g phenol in 500 ml 50 mM sodium acetate (pH 4.0). Once dissolved, let phases separate and remove upper aqueous phase. Add 500 ml 50 mM sodium acetate (pH 4.0); stir to emulsify and let phases separate. Repeat procedure until the pH of upper, aqueous phase is less than pH 4.1. Store at 4C protected from light. Caution: Phenol is highly corrosive and can cause severe burns. Always wear gloves, protective clothing and safety glasses when working with phenol. If skin comes in contact with phenol, immediately wash with a large volume of water and soap.
156
5.1.
Buffers
Electrophoresis of Proteins
10% Ammonium persulfate 10 ml 30% acryl-bisacrylamide mix 100 ml
Dissolve 1 g ammonium persulfate (APS) in 8 ml H2O. Adjust volume to 10 ml with H2O. Solution is stable at 4C for two weeks. Dissolve 29 g acrylamide and 1 g N,N-methylenebisacrylamide in 60 ml H2O. Heat the solution to 37C to dissolve the chemicals. Adjust volume to 100 ml with H2O. Store at 4C protected from light. Caution: Acrylamide is a neurotoxin and is absorbed through the skin. Always wear gloves and a mask when preparing the solutions. Mix 10 ml 1.5 M Tris (pH 6.8), 6 ml 20% SDS, 30 ml glycerol, 15 ml -mercaptoethanol and 1.8 mg bromophenol blue. Adjust volume to 100 ml with H2O. Aliquot in 10 ml stock solution and store at 20C. Store working solution at 4C.
2 x SDS PAGE sample buffer 100 ml
10 x SDS PAGE Running buffer 1 liter Coomassie Blue staining solution 1 liter Coomassie Blue destaining solution 1 liter
Dissolve 10 g SDS, 30.3 g Tris and 144.1 g glycin in 800 ml H2O. Adjust volume to 1 liter with H2O. Store at room temperature. Dissolve 2.5 g Coomassie Brilliant Blue R-250 in a mixture of 450 ml methanol, 100 ml acetic acid and 400 ml H2O. Adjust volume to 1 liter with H2O. Store at room temperature. Mix 450 ml methanol, 100 ml acetic acid and 400 ml H2O. Adjust volume to 1 liter with H2O. Store at room temperature.
157
5.1.
Buffers
Resolving gels for denaturing SDS PAGE
Volume of components (ml) per gel mold volume of Components H 2O 30% acryl-bisacrylamide mix 1.5 M Tris (pH 8.8) 10% SDS 10% ammonium persulfate TEMED H 2O 30% acryl-bisacrylamide mix 1.5 M Tris (pH 8.8) 10% SDS 10% ammonium persulfate TEMED H 2O 30% acryl-bisacrylamide mix 1.5 M Tris (pH 8.8) 10% SDS 10% ammonium persulfate TEMED H 2O 30% acryl-bisacrylamide mix 1.5 M Tris (pH 8.8) 10% SDS 10% ammonium persulfate TEMED H 2O 30% acryl-bisacrylamide mix 1.5 M Tris (pH 8.8) 10% SDS 10% ammonium persulfate TEMED 5 ml 2.6 1.0 1.3 0.05 0.05 0.004 2.3 1.3 1.3 0.05 0.05 0.003 1.9 1.7 1.3 0.05 0.05 0.002 1.6 2.0 1.3 0.05 0.05 0.002 1.1 2.5 1.3 0.05 0.05 0.002 10 ml 5.3 2.0 2.5 0.1 0.1 0.008 4.6 2.7 2.5 0.1 0.1 0.006 4.0 3.3 2.5 0.1 0.1 0.004 3.3 4.0 2.5 0.1 0.1 0.004 2.3 5.0 2.5 0.1 0.1 0.004 15 ml 7.9 3.0 3.8 0.15 0.15 0.012 6.9 4.0 3.8 0.15 0.15 0.009 5.9 5.0 3.8 0.15 0.15 0.006 4.9 6.0 3.8 0.15 0.15 0.006 3.4 7.5 3.8 0.15 0.15 0.006 20 ml 10.6 4.0 5.0 0.2 0.2 0.016 9.3 5.3 5.0 0.2 0.2 0.012 7.9 6.7 5.0 0.2 0.2 0.008 6.6 8.0 5.0 0.2 0.2 0.008 4.6 10.0 5.0 0.2 0.2 0.008 25 ml 13.2 5.0 6.3 0.25 0.25 0.02 11.5 6.7 6.3 0.25 0.25 0.015 9.9 8.3 6.3 0.25 0.25 0.01 8.2 10.0 6.3 0.25 0.25 0.01 5.7 12.5 6.3 0.25 0.25 0.01 30 ml 15.9 6.0 7.5 0.3 0.3 0.024 13.9 8.0 7.5 0.3 0.3 0.018 11.9 10.0 7.5 0.3 0.3 0.012 9.9 12.0 7.5 0.3 0.3 0.012 6.9 15.0 7.5 0.3 0.3 0.012 40 ml 21.2 8.0 10.0 0.4 0.4 0.032 18.5 10.7 1.0 0.4 0.4 0.024 15.9 13.3 10.0 0.4 0.4 0.016 13.2 16.0 10.0 0.4 0.4 0.016 9.2 20.0 10.0 0.4 0.4 0.016 50 ml 26.50 10.00 12.50 0.50 0.50 0.04 23.20 13.30 12.50 0.50 0.50 0.03 19.80 16.70 12.50 0.50 0.50 0.02 16.50 20.00 12.50 0.50 0.50 0.02 11.50 25.00 12.50 0.50 0.50 0.02
% Gel 6%
8%
10%
12%
15%
5% stacking gels for denaturing SDS-PAGE

Volume of components (ml) per gel mold volume of Components 1 ml H2O 30% acryl-bisacrylamide mix 1.5 M Tris (pH 6.8) 10% SDS 10% ammonium persulfate TEMED 0.68 0.17 0.13 0.01 0.01 0.001 2 ml 1.4 0.33 0.25 0.02 0.02 0.002 3 ml 2.1 0.5 0.38 0.03 0.03 0.003 4 ml 2.7 0.67 0.5 0.04 0.04 0.004 5 ml 3.4 0.83 0.63 0.05 0.05 0.005 6 ml 4.1 1.0 0.75 0.06 0.06 0.006 8 ml 5.5 1.3 1.0 0.08 0.08 0.008 10 ml 6.8 1.7 1.25 0.1 0.1 0.01
158
5.1.
Buffers
Western Blotting
1x Transfer Buffer for wet blots 1 liter 1x Transfer Buffer for semi-dry blots
Dissolve 2.9 g Glycine, 5.8 g Tris and 0.37 g SDS in 200 ml methanol. Adjust volume to 1 liter with H2O. Store at 4C.
Scheme:
Layer 5 (top) 4 3 2 1 (bottom) Content and Buffer 3 x 3 MM papers soaked in 300 mM Tris, pH 10.4 membrane gel 3 x 3 MM papers soaked in 25 mM Tris, pH 9.4 and 40 mM amino hexane acid 3 x 3 MM papers soaked in 25 mM Tris, pH 10.4
Ponceau S Solution 100 ml
Mix 2 g Ponceau S, 30 g trichloracetic acid and 30 g sulfosalicylic acid in 80 ml H2O. Adjust volume to 100 ml with H2O. Store at room temperature.
1 x TBS (Tris Buffered Saline) 1 liter
Dissolve 6.05 g Tris (50 mM) and 8.76 g NaCl (150 mM) in 800 ml H2O. Adjust pH to 7.5 with 1 M HCl (~ 9.5 ml). Adjust volume to 1 liter with H2O. TBS is stable at 4C for three months. Note: Since sodium azide inhibits peroxidase activity, it is not recommended for use as an antimicrobial reagent. Dissolve 1 ml Tween 20* in 1 liter TBS buffer. TBST is stable at 4C for three months. Note: Tween 20 is suitable for most applications but depending on the type of membrane and antibodies used, different detergents (like SDS*, Triton X100* or Nonidet P40*) and concentrations between 0.01 1% may lead to better results. A wide variety of different blocking solutions are described in the literature. A solution of 2.5 to 5% (w/v) nonfat dried milk in TBS or PBS is sufficient for most blots. If background is high, use alternative blocking solutions* containing 1% of e.g., BSA, gelatine or casein.
1 x TBST (Tris Buffered Saline Tween) 1 liter
Blocking solution*
159
5.2.
Antibiotic Ampicillin (Amp)
Antibiotics
Selection of prokaryotic cells
Mode of Action Inhibits cell wall synthesis by inhibiting formation of the peptidoglycan cross-link. Prevents peptide bond formation by binding to the 50S subunit of ribosomes. Causes misreading of mRNA by binding to 70S ribosomes. Mechanism of Resistance The resistance gene (bla) specifies an enzyme, -lactamase, which cleaves the -lactam ring of the antibiotic. The resistance gene (cat) specifies an acetyltransferase that acetylates and thereby inactivates the antibiotic. The resistance gene (kan) specifies an aminoglycoside phosphotransferase that inactivates the antibiotic. The resistance gene (str) specifies an enzyme that modifies the antibiotic and inhibits its binding to the ribosomes. The resistance gene (tet) specifies a protein that modifies the bacterial membrane and prevents transport of the antibiotic into the cell. Working Concentrationa 20 100 g/ml (50 g/ml) Stock Solutionb 100 mg/ml in H2O Store at 20C.
Chloramphenicol (Cm) Kanamycin (Kan)
25 170 g/ml (100 g/ml)
34 mg/ml in Ethanol Store at 20C.
10 50 g/ml (30 g/ml)
30 mg/ml in H2O Store at 20C.
Streptomycin Causes misreading of mRNA (Sm) by binding to 30S subunit of ribosomes. Tetracycline (Tet) Prevents protein synthesis by preventing binding of the aminoacyl tRNA to the ribosome A site.
10 125 g/ml (50 g/ml)
50 mg/ml in H2O Store at 20C.
10 50 g/ml 12.5 mg/ml in Ethanol (10 g/ml in liquid Store at 20C. culture 12.5 g/ ml in plates)
a lower b stock
concentrations: for the selection of plasmids with a low copy number, higher concentrations: for the selection of plasmids with a high copy number, values in brackets indicate commonly used concentrations. solutions in H2O: sterilize by filtration and store protected from light. Stock solutions in ethanol should not be sterilized.
Selection of eukaryotic cells

Antibiotic Geneticin (G 418) Mode of Action Interferes with the function of 80S ribosomes and blocks protein synthesis in eukaryotic cells. Mechanism of Resistance The resistance gene (neo) encodes a bacterial aminoglycoside phosphotransferase that inactivates the antibiotic. The resistance gene specifies an aminoglycoside phosphotransferase that inactivates the antibiotic. The resistance gene (hyg or hph) codes for a kinase that inactivates Hygromycin B through phosphorylation. Working Concentration 50 1000 g/ml; optimal concentration is to be tested experimentallyb 100 g/ml Stock Solutiona 5 50 mg/ml in culture medium or physiological buffers Store at 20C 10 50 mg/ml solution in H2O. Store at 4C 50 mg/ml in PBS Store at 4C
Gentamycin
Inhibits protein synthesis by binding to the L6 protein of the 50S ribosomal subunit. Inhibits protein synthesis of bacteria, fungi and eukaryotic cells by interfering with translocation and causing mistranslation.
Hygromycin B
50 1000 g/ml; optimal concentration is to be tested experimentallyb
a stock
solutions in H2O, culture medium, physiological buffers or PBS: sterilize by filtration, store protected from light. Stock solutions in ethanol should not be sterilized. b a table with optimal cell-line specific concentrations is available from Roche Applied Science.
160
5.3.
LB
Media for Bacteria

Recipes for 1 liter
Mix 10 g Bacto-Tryptone, 5 g Bacto-Yeast extract and 10 g NaCl in 900 ml H2O. Adjust the pH to 7.0 with 10 M NaOH (~ 200 l). Adjust volume to 1 liter with H2O. Sterilize by autoclaving and store at room temperature. Mix 12.8 g Na2HPO4 7H2O, 3 g KH2PO4, 0.5 g NaCl and 1 g NH4Cl in 750 ml H2O. Adjust the pH to 7.4 with 10 M NaOH (~ 100 l). Adjust volume to 1 liter with H2O. Sterilize by autoclaving and cool to room temperature. Add 2 ml 1 M MgSO4 7H2O, 0.1 ml 1 M CaCl2 and 10 ml 20% glucose. Sterilize by filtration and store at room temperature. Mix 20 g Bacto-Tryptone, 5 g Bacto-Yeast extract, 0.5 g NaCl and 2.5 ml 1 M KCl in 900 ml H2O. Adjust pH to 7.0 with 10 M NaOH (~ 100 l) and add H2O to 990 ml. Sterilize by autoclaving and store at room temperature. Before use, add 10 ml sterile 1 M MgCl2.
M9 minimal
SOB
SOC TB
Identical to SOB medium, except that it additionally contains 20 ml sterile 1 M glucose. Mix 12 g Bacto-Tryptone, 24 g Bacto-Yeast extract and 4 ml glycerol in 900 ml H2O. Sterilize by autoclaving and cool to < 60C. Add 100 ml of sterile 10 x TB phosphate* and store at room temperature. Mix 8 g Bacto-Tryptone, 5 g Bacto-Yeast extract and 2.5 g NaCl in 900 ml H2O. Adjust pH to 7.0 with 10 M NaOH (~ 200 l). Adjust volume to 1 liter with H2O. Sterilize by autoclaving and store at room temperature.
YT
* Made by dissolving 2.31 g KH2PO4 (= 0.17 M) and 12.54 K2HPO4 (= 0.72 M) in 90 ml H2O. Adjust volume to 100 ml with H2O and sterilize by autoclaving. Store at room temperature.
161
5.3.
Media for Bacteria

Recipes for 1 liter (for 40 plates of 90 mm, 25 ml per plate)
Agar plates
Prepare liquid media according to the recipes given on page 161. Add 15 g Bacto-Agar to 1 liter liquid medium and sterilize by autoclaving. Allow the medium to cool to 50C and add the appropriate amount of antibiotic (see chapter 5.2., page 160, for the best concentration of antibiotic). Gently mix the medium by swirling and pour into sterile plates. Flame the surface of the medium in the plates with a bunsen burner to remove air bubbles. Allow the medium to solidify and store the dishes at 4C in the inverted position. Store tetracycline plates in the dark. Use a color code to indicate the type of antibiotic in the plate (e.g., black stripe for ampicilin plates, blue stripe for kanamycin plates, ). Before use, incubate plates at 37C in the inverted position for 1 hour to remove condensation within the plate.
X-gal/IPTG indicator plates
Before pouring the plates, add: 2 ml of IPTG stock solution (0.1 M) final concentration: 0.2 mM 2 ml of X-gal stock solution (20 mg/ml) final concentration: 40 g/ml Prepare liquid media according to the recipes given on page 161. Add 7 g Bacto-Agar to 1 liter liquid medium and sterilize by autoclaving.
Top agar overlay
162
5.4.
1. 2. 3. 4. 5. 6.
References
Ausubel, F. M. et al., (1991) In: Current Protocols in Molecular Biology. John Wiley and Sons, New York Brown, T. A. (1991) In: Molecular Biology LabFax. Bios Scientific Publishers, Academic Press Fluka (1998), MicroSelect: Basics for Biochemistry and Molecular Biology Good, N. E. , Izawa, S. (1972) In: Methods in Enzymology, 24, 53 68 Roche Applied Science, Technical Data Sheets Sambrook. J., Fritsch, E. J. and Maniatis, T. (1989) In: Molecular Cloning, A Laboratory Manual, 2nd edition. Cold Spring Harbor Laboratory Press
Conversion Tables and Formulas

Chapter 6
6.1. Nucleotide ambiguity code.......................................... 6.2. Formulas to calculate melting temperatures ....... 6.3. %GC content of different genomes ......................... 6.4. Metric prefixes ................................................................ 6.5. Greek alphabet ................................................................ 6.6. Properties of radioisotopes ......................................... 6.7. Temperatures and Pressures ..................................... 6.8. Centrifugal forces ........................................................... 6.9. Periodical system of elements ................................... 6.10. Hazard Symbols .............................................................. 6.11. References ........................................................................
164 164 165 165 166 166 167 167 168 168 169
6.1.
Nucleotide ambiguity code

Code A G C T Y R W S K M D V H B X/N Represents Adenosine Guanine Cytosine Thymidine Pyrimidine (C & T) Purine (A & G) weak (A & T) strong (G & C) keto (T & G) amino (C & A) not C not T not G not A unknown Complement T C G A R Y W S M K H B D V X/N
6.2.
Systema
Formulas to calculate melting temperature T m

Formulab Tm = 81.5C + 16.6 log[Na+] + 0.41 (%GC) 0.61 (%for) 500/N Tm = 79.8C + 18.5 log[Na+] + 0.58 (%GC) + 11.8 (%GC)2 0.50 (%for) 820/N Tm = 79.8C + 18.5 log[Na+] + 0.58 (%GC) + 11.8 (%GC)2 0.35 (%for) 820/N
DNA DNA hybrids (see reference 6) DNA RNA hybrids (see reference 7) RNA RNA hybrids (see reference 8) Oligonucleotides (see reference 9)
For oligonucleotides 14 25 nucleotides in length:

Tm = [2C x (number of A and T bases)] + [4C x (number of G and C bases)]
For Oligonucleotides longer than 25 nucleotides: see formula for DNA/DNA hybrids
a The proposed b +
formula is valid for Na+ concentrations between 0.01 0.4 M and %GC values between 30 75% [Na ] = concentration of Na+ ions, %GC = percentage of G and C nucleotides in the nucleic acid, %for = percentage of formamide in the hybridisation solution, N = length of the duplex in base pairs
164
6.3.
%GC content of different genomes

%GC content Organism Vertebrates 34.6 49.6 47.4 48.6 Homo Sapiens Xenopus laevis Mus musculus Rattus species 40.3 40.9 40.3 41.8 %GC content
Organism Phages T2 T3 T7 Lambda Prokaryotes Agrobacterium tumefaciens Bacillus subtilis Escherichia coli Mycobacterium tuberculosis Staphylococcus aureus
58 59.7 42.6 51 65 32.4 37.7
6.4.
10 10
Metric prefixes
Factor
18 15
Prefix exa peta tetra giga mega kilo milli micro nano pico femto atto
Symbol E P T G M k m n p f a 1 * =10-10 m 10-8 cm 10-4 m 10-1 nm * Named after Anders J. ngstrm (1814 1874), a famous Swedish spectroscopist
10 12 10
9
10 6 103 10-3 10-6 10

-9
10-12 10
-15
10-18
Examples:
1 ng (nanogram) = 10-9 gram 5 pmol (picomole)= 10-12 mol

165
6.5.
Greek alphabet
alpha beta gamma delta epsilon zeta eta theta iota kappa lambda mu nu xi omicron pi rho sigma tau upsilon phi chi psi omega
6.6.
Isotope
Properties of radioisotopes
Halflifea Decayb Maximum range in air (cm) EC EC 790 46 30 0.6 52 24 Protection Detectionc Autoradio- Fluorography graphy cpm cpm needed needed overnight overnight Fluorography method
Calcium-45 Carbon-14
45
Ca C
164 d 5730 y 27.7 d 59.6 d 14.3 d 25.3 d 87.4 d 12.4 y
acrylic shield acrylic shield lead shield lead shield acrylic shield acrylic shield acrylic shield
GM, LS LS,P LS,P GM, LS GM, LS GM, LS GM LS

a d b
14
2,000
200
PPO impregnated gel ( 70C)
Chromium-51 51Cr Iodine-125 Phosphor-32 Phosphor-33 Sulphur-35 Tritium

125
100 50 1,000 1,000 >107
10 10 100 200 100 200 3,000
screen ( 70C) screen ( 70C) PPO impregnated gel ( 70C) PPO impregnated gel ( 70C) PPO impregnated gel ( 70C)
32P 33
P S
35
3H
Units: 1 Ci = 2.2 x 10 6 desintegrations/minute = 3.7 x 10 4 becquerels (Bq) 1 Becquerel = 1 desintegration/second Dosis: 1 Gray (Gy) = 100 rad 1 Sievert (Sv) = 100 rem
= days, y = years = beta radiation EC = electron capture c GM = Geiger-Mller detector LS = liquid scintillation P = End window
166
6.7 .
Temperatures and Pressure

From Centigrade to Fahrenheit F = 32 + (C x 9 ) 5 From Fahrenheit to Centigrade C = 5 x (F 32) 9
From millibars (mbar) to Millimeters of mercury (mm Hg) Inches of mercury (inch Hg) Pounds per square inch (psi) Atmospheres (atm) Kilopascals (kPa) Torrs (Torr)
Multiply by 0.750000 0.039400 0.014500 0.000987 0.100000 0.750000
6.8.
Centrifugal forces
Nomogram:
link between revolutions/minute, centrifugal force and rotor radius Mathematical:

RCF 1.12 x R rpm
rpm = 1000
RCF = 1.12 x R( 1000 )2 where rpm = revolutions per minute of rotor RCF = relative centrifugal force R = radius of rotor in mm at room temperature
Align a straight line through known values in two columns and read desired value in third column
167
6.9.
Periodical System of Elements
6.10. Hazard Symbols and Risk Phrases

Symbol
Flammable
Hazard
Spontaneously flammable substances. Chemicals igniting in air. Gases, gas mixtures (also liquefied ones) which have an ignition range with air at normal pressure. Substances sensitive to moisture. Chemicals which readily from flammable gases on contact with water.
Caution
Avoid contact with air. Avoid formation of flammable gas-air mixture. Avoid contact with moisture water.
Symbol
Harmful or Irritant
Hazard
Inhalation and ingestion of, or skin penetration by these substances is harmful to ones health. Non-recurring, recurring, or lengthy exposure to these substances may result in irreversible damage. This symbol designates substances which may have an irritant effect on skin, eyes, and respiratory organs.
Caution
Avoid contact with the human body, including inhalation of the vapors and in cases of malaise, consult a doctor. Do not breathe vapors and avoid contact with skin and eyes. Do not breathe vapors and avoid contact with skin, eyes, and clothing.
Liquids with flash point below 21C. Keep away from open fires, sources of heat and sparks Solid substances which ignite easily after a short term effect of a source of ignition.
Oxidizing
Corrosive
Avoid all contact with all sources of ignition. Keep away from combustible material.
Toxic
Living tissue as well as equipment are destroyed on contact with these chemicals.
Oxidizing substances can ignite combustible material or worsen existing fires and thus make firefighting more difficult.
Explosive
This symbol designates substances which may explode under definite conditions.
Avoid shock, friction, sparks, and heat.
The substances are very hazardous to health when breathed, swallowed, or in contact with the skin and may even lead to death. Non-recurring, recurring, or lengthy exposure to these substances may result in irreversible damage.
Avoid contact with the human body and immediately consult a doctor in cases of malaise.
168
6.11. References
1. 2. 3. 4. 5. 6. 7. 8. 9. Ausubel, F.M. et al., (1991) In: Current Protocols in Molecular Biology. John Wiley and Sons, New York Biochemica Information (1987) Roche Applied Science Brown, T. A. (1991) In: Molecular Biology LabFax. Bios Scientific Publishers, Academic Press Roche Applied Science, Technical Data Sheets Sambrook. J., Fritsch, E. J. and Maniatis, T. (1989) In: Molecular Cloning, A Laboratory Manual, 2nd edition Cold Spring Harbor Laboratory Press Meinkoth, J. et al., (1984) Anal. Biochem., 138, 267 Casey, J., et al., (1977) NAR, 4, 1539 Wallace, R. B., et al., (1979) NAR, 6, 3543 Thein, S. L., et al., (1986) Human Genetic Diseases, a practical approach, IRL Press, Virginia
Addresses, Abbreviations and Index

Chapter 7
7.1. 7.2. 7.3. 7.4.
Selection of useful addresses ...................................... Lab Steno............................................................................. Abbreviations ..................................................................... Alphabetical Index............................................................
170 172 173 176
7.1.
Name
Selection of useful addresses*

Internet address http://arabi4.agr.hokudai.ac.jp/Links/Links.html# At_genome http://www.atcc.org http://www.expasy.ch/tools/pathways/ http://biocyc.org/ http://www.biochem.ucl.ac.uk/bsm/cath http://www.ncbi.nlm.nih.gov/dbEST/index.html Contains information on Genomic and related data, physical and genetic maps of Arabidopsis thaliana American type culture collection The internet version of the traditional Boehringer Mannheim wall chart. BioCyc is a collection of 260 Pathway/Genome Databases. Hierarchical domain classification of protein structures Sequence data and other information on single pass cDNA sequences or expressed sequence tags from a number of organisms Encyclopedia of E.coli genes and metabolism PubMed/MEDLINE Protein DB Nucleotide DB NM3D (data from crystallographic and NMR structural determinations) Database of the Drosophila Genome
Arabidopsis ATCC Biochemical Pathways BioCyc CATH dbEST
EcoCyc ENTREZ
http://ecocyc.org/ http://www.ncbi.nlm.nih.gov/Entrez
Flybase
http://flybase.bio.indiana.edu/
Name GDB
Internet address http://www.gdb.org
Contains information on Location of human genes, DNA fragments, fragile sites and breakpoints Populations, polymorphisms, maps and mutations Genetic sequence database automatically collected of publicly available sequences Enzyme reactions Chemical compounds Metabolic pathways with links to gene catalogues. Genetics of laboratory mouse. Human genes and genetic disorders 3D coordinates of macromolecular structures. Restriction enzymes and methylases
Genbank KEGG/ LIGAND MGD Omim PDB REBASE
http://www.ncbi.nlm.nih.gov/genbank http://www.genome.ad.jp/kegg/kegg.html http://www.genome.ad.jp/dbget/ligand.html http://www.informatics.jax.org http://www.ncbi.nlm.nih.gov/omim/ http://www.rcsb.org/pdb/ http://rebase.neb.com
* Web sites continually appear, disappear and change addresses, quickly invalidating any list of useful sites. All of the web sites given here were operating in July, 2007.
170
7.1.
Name
Selection of useful addresses*

Internet address http://www.restriction-enzymes.com http://www.roche-applied-science.com
(continued)
Contains information on Tools for Mapping & Cloning total product portfolio, online technical support and e-shop available from Roche Applied Science. Structural classification of protein domains Protein sequences obtained or translated from nucleotide sequences, including descriptions of protein functions, domain structure, posttranslational modifications, Design real-time qPCR assays in seconds. Comprehensive Yeast Genome Database, annotated complete DNA sequence of Saccharomyces cerevisiae
Restriction Enzymes Roche Applied Science SCOP SWIS-PROT
http://scop.mrc-lmb.cam.ac.uk/scop http://www.expasy.ch/sprot
Universal ProbeLibrary Yeast
http://www.universalprobelibrary.com http://mips.gsf.de/proj/yeast/
For information on Gateway to North American Libraries PCR and multiplex PCR: guide and troubleshooting
Web address http://lcweb.loc.gov/z3950/gateway.html http://www.roche-applied-science.com
* Web sites continually appear, disappear and change addresses, quickly invalidating any list of useful sites. All of the web sites given here were operating in July, 2007.
171
7.2.
Lab Steno
Explanation centrifuge mix over head shake vortex rotate / mixing by turn over do for (time) at (number) C next step add discard divide into digest digest pUC19 with BamH I add 5 ml buffer A Example Translation spin at 13 000 g-force mix 5times over head shake for 3 minutes vortex for 15 seconds rotate the sample for 15 minutes incubate for 5 min at 4C
Symbol
Symbol
Explanation precipitate / pelletate pellet supernatant buffer / solution interrupt stop (monoclonal) antibody anti mouse rabbit negative/positive
Example
Translation
redisolve pellet in 5 ml buffer A
buffer B
antibody against HIS 2nd anti mouse POD rabbit anti mouse sheep anti rabbit reaction #5 is negative
172
7.3.
A
Abbreviations
B
BCIP bp Bq Br-UTP BrdU BSA 5-Bromo-4-chloro-3-indolyl-phosphate Base pair(s) Becquerel 5-Bromo-uridine-5'-triphosphate 5-Bromo-2'-deoxyuridine Bovine serum albumin
A adenine or adenosine Absorbance unit ( 50 g for double-stranded DNA) A260 unit AAS Atomic absorption spectrophotometry Ab antibody ABTS 2,2-Azino-di-[3-ethylbenzthiazoline sulfonate (6)] Acetyl-CoA Acetyl-coenzyme A ADA Adenosine deaminase ADH Alcohol dehydrogenase ADP Adenosine-5'-diphosphate Agarose LE Agarose low electroendosmosis Agarose LM-MP Low melting point multi purpose agarose Agarose MP Multi purpose agarose AIDS Acquired immunodeficiency syndrome Ala L-Alanine AMP adenosine monophosphate AMV Avian myeloblastosis virus AOD Amino acid oxidase AP Akaline phosphatase APMSF (4-Amidinophenyl)-methane-sulfonyl fluoride Arg L-Arginine Arg-C Endoproteinase, arginine-specific Asn L-Asparagine Asp L-Aspartic acid ATP Adenosine-5'-triphosphate
C
C CAT cDNA CHAPS Ci CK CL CMC CMP CoA cpm CSPD cytosine or cytidine Chloramphenicol acetyltransferase Complementary DNA 3-[(3-Cholamidopropyl)-dimethyl-ammonio]-1-propane sulfonate Curie Creatine kinase Citrate lyase Critical micellar concentration Cyclic monophosphate Coenzyme A Counts per minute Disodium 3-(4-methoxyspiro{1,2-dioxetane-3,2'(5'-chloro)-tricyclo[3.3.1.13'7]decan}-4-yl)phenyl phosphate Cytidine-5'-triphosphate L-Cysteine Cytochrome c
CTP Cys cyt-c
D
dADP dAMP DAPI dATP dCDP dCTP ddATP ddCTP ddGTP ddNTP ddTTP ddUTP dCDP dGMP dGTP DIG DIN dITP DL DMF DMSO DNA DNase dNTP dpm 2'-Deoxyadenosine-5'-diphosphate 2'-Deoxyadenosine-5'-monophosphate 4',6-Diamidine-2'-phenylindole dihydrochloride 2'-Deoxyadenosine-5'-triphosphate 2'-Deoxycytidine-5'-diphosphate 2'-Deoxycytidine-5'-triphosphate 2',3'-Dideoxyadenosine-5'-triphosphate 2',3'-Dideoxycytidine-5'-triphosphate 2',3'-Dideoxyguanosine-5'-triphosphate Dideoxynucleoside triphosphate 2',3'-Dideoxythymidine-5'-triphosphate 2',3'-Dideoxyuridine-5'-triphosphate 2'-Deoxyguanosine-5'-diphosphate 2'-Deoxyguanosine-5'-monophosphate 2'-Deoxyguanosine-5'-triphosphate Digoxigenin German standards 2'-Deoxyinosine-5'-triphosphate Dosis lethal Dimethylformamide Dimethyl sulfoxide Deoxyribonucleic acid Deoxyribonuclease Deoxynucleoside triphosphate Decays per minute
ds dTDP DTE dTMP DTT dTTP dU dUTP
Double-stranded (DNA) Thymidine-5'-diphosphate 1,4-Dithioerythritol Thymidine-5'-monophosphate 1,4-Dithiothreitol Thymidine-5'-triphosphate Deoxy-uridine 2'-Deoxy-uridine-5'-triphosphate
E
E. coli EC EDTA EGTA EIA ELISA EPO Absorptivity (absorption coefficient) Escherichia coli Enzyme classification (enzyme commission) number Ethylenediamine tetraacetic acid Ethyleneglycol-bis-(2-aminoethylether)-N,N,N',N' tetraacetic acid Enzyme immunoassay Enzyme-linked immunoabsorbent assay Erythropoietin
F
F(ab')2 Fab FACS FAD Variable sequence fragment of immunoglobulin, generated by pepsin Variable sequence fragment of immunoglobulin, generated by papain Fluorescence-activated cell sorting Flavin adenine dinucleotide
173
FC FITC FLUOS FMN fmol FRET+
Flow cytometry Fluorescein isothiocyanate 5(6)-Carboxyfluorescein-N-hydroxysuccinimide ester Flavin mononudeotide femto mol Fluorescence Resonance Energy Transfer
IL IL-2R Ile INT IR ISH lU
G
G -Gal GDP Gln Glu Glu-C Gly GMP GTP guanine or guanosine -Galactosidase Guanosine-5'-diphosphate L-Glutamine L-Glutamic acid Endoproteinase, glutamic acid specific L-Glycine Guanosine-5'-monophosphate Guanosine-5'-triphosphate
Interleukin Interleukin 2-receptor L-lsoleucine 2-(4-Iodophenyl)-5-(4-nitrophenyl)-3-phenyl-tetrazolium chloride lnfrared spectroscopy In situ hybridization International unit
K
kbp kBq kD Kilobase pair(s) Kilobecquerel Kilo Dalton
L
LD Leu Ile Lys Lys-C Lethal dosis L-Leucine L-lsoleucine L-Lysine Endoproteinase, Iysine-specific
H
Hepes Hg His HIV HPLC HRP 4-(2-Hydroxyethyl)-1-piperazineethanesulfonic acid Mercury L-Histidine Human immunodeficiency virus High pressure liquid chromatography Horse radish peroxidase
M
-ME MBq Mes Met mg g l M -Mercaptoethanol Megabecquerel 4-Morpholineethanesulfonic acid L-Methionine milligram (10-3 g) microgramm (10-6 g) microliter (10-6 L) micromolar (10-6 M)
I
Ig IH IHC/ICC Immunoglobulin lmmunohistochemistry lmmunohisto/cytochemistry
ml mm mM mRNA MTP MW
milliliter (10-3 L) millimeter (10-3 m) millimolar (10-3 M) Messenger RNA Microtiter plate molecular weight
ppm Pro PVDF
Parts per million L-Proline PoIyvinylidene-difluoride
R
RACE RARE RE RNA RNase RT Rapid amplification of cDNA ends recA-assisted restriction endonuclease cleavage Restriction enzyme Ribonucleic acid Ribonuclease Reverse transcriptase
N
NBT NC nm nmol 4-Nitro blue tetrazolium chloride Nitrocellulose Nanometer nanemole (10-9 mole)
O
ONPG 2-NitrophenyI- -O-gaIactopyranoside
S
SDS-PAGE SDS Ser ss Sodium dodecyl sulfate polyacrylamid gel electrophoresis Sodium dodecyl sulfate L-Serine Single-stranded (DNA)
P
PAGE PCR PEG PFGE pg Phe pI pmol PMSF POD Polyacrylamide gel electrophoresis Polymerase Chain Reaction Polyethylene glycol Pulsed field gel electrophoresis picogram (10-12 g) L-Phenylalanine Isoelectric point picomole (10-12 mole) Phenyl-methyl-sulfonyl fluoride Peroxidase
T
T TAE TBE TBq TCA TEA Thr thymine or thymidine Tris-acetate-EDTA Tris-borate-EDTA Terabecquerel Trichloroacetic acid Triethanolamine L-Threonine
174
TM TMB TPCK Tris tRNA Tyr
Melting temperature Tetramythylbenzidine N-TosyI-L-phenyl-alanine-chloromethyl ketone Tris(hydroxymethyl)-amino-methane Transfer ribonucleic acid L-Tyrosine
W
w/v WB Weight/volume Western (protein) blots
X
X-Gal X-Gluc X-phosphate XTT 5-Bromo-4-chIoro-3-indoIyI- -D-galactopyranoside 5-Bromo-4-chIoro-3-indoIyI- -D-glucuronic acid 5-Bromo-4-chloro-3-indolyl-phosphate Sodium 3'-[1-(phenyl-amino-carbonyl)-3,4-tetrazolium]-bis (4-methoxy-6-nitro)-benzene soIfonic acid hydrate
U
U U UDP UTP UV Unit (of enzyme activity) uracil or uridine Uridine-5'-diphosphate Uridine-5'-triphosphate Ultraviolet
Y
YAC Yeast Artificial Chromosome
V
v/v Val Volume/volume L-Valine
Notes
175
7.4.
Alphabetical index
The colors of the topics refer to the color code of the respective chapter.
A
Acrylamide-bisacrylamide, recipe recipe to prepare resolving and stacking gels Agar plates, recipe Amino Acids, characteristics of Ammonium acetate buffer, recipe Ammonium persulfate, recipe Ampicillin, general information Amplification of DNA: see PCR Antibiotics, ampicillin, general information chloramphenicol, general information geneticin, general information gentamycin, general information hygromycin, general information kanamycin, general information streptomycin, general information tetracyclin, general information 157 158 162 90 148 157 160 160 160 160 160 160 160 160 160
Antibodies, choices of animals for immunization different sources doses of immunogens for rabbits purification via immunoprecipitation routes of injections for rabbits Apoptosis / Necrosis Apoptosis Assay Method APS, recipe
105 102 106 107 106 131 134 157
B
Bacterial cell: nucleic acid and protein content Bacterial Strains (commonly used) Blood: nucleic acid and protein content Buffer exchange via gel filtration Buffers, calculating molarities and concentrations precautions purity of reagents and H2O sterilizing pH measurement pH range of commonly used buffers
119 27, 28 120 94 146 146 146 146 147 148
176
C
CaCl2, recipe Cell Cycle Cell Proliferation and Viability Centrifugal forces, calculation of Chloramphenical, general information Codon Usage Complete Concentration of DNA via OD measurement Concentration of Proteins, interfering substances via OD measurement Concentration of RNA via OD measurement Conversion of DNA from pmol to g and g to pmol, calculation Conversion of RNA from pmol to g and g to pmol, calculation Conversion from Nucleic Acids to Proteins Amino Acids Codon Usage Genetic Code Information Transfer Conversion of pressure Conversion of temperatures between Centrigrade and Fahrenheit Coomassie Blue staining and destaining solution Culture vessels: growth areas and yields of cells 148 121 136 167 160 91 85 9 100 98 68 4 63 88 91 89 88 167 167 157 115
D
Denhardt solution, recipe DEPC, treatment Dephoshorylation of DNA Detection of mycoplasma contamination Detection of Proteins on membranes Detergents, commonly used general properties removal of Dialysis of Proteins DIG Labeling of Nucleic Acids Dissolving of DNA Dissolving of RNA DNA Polymerase I for nick translation DNA purification,MagNA Pure LC Instrument Drying of DNA Drying of RNA DTT, recipe 148 155 23 116 93 94 94 96 94 31 2 62 33 8 2 61 148
177
E
EDTA, recipe Electroporation Ethidum bromide, recipe Expression of Proteins, characteristics of different systems 149 128 156 103
F
Fill-in 3and 5recessed ends of DNA Fluorescence activated cell sorting Fluorescence Resonance Energy Transfer 24 138 50
G
GC content of different genomes Genetic Code Geneticin, general information Gentamycin, general information Greek alphabet Growth areas and yields of cellsa in a cultural vessel 165 89 160 160 166 115
H
Handling of DNA Handling of RNA Hybridization Probes HybProbe Format Hygromycin, general information 2 60 48 50 160
I
Immunoprecipitation of antibodies Ion exchange chromatography of proteins IPTG, recipe Isolation of DNA MagNA Pure LC Instrument product application table product characteristics table product selection table Isolation of RNA MagNA Pure LC Instrument Isolation of RNA product application table product characteristics table product selection table
107 109 149 8 6 7 6 8 65 66 65
178
K
Kanamycin, general information Klenow to fill-in 3recessed ends of DNA for random primed labeling of DNA KOAc, recipe for buffer with desired pH K phosphate, recipe for buffer with desired pH 160 24 32 152 153
L
Labeling of DNA Choice of labeling method 3End labeling with Terminal Transferase 5End labeling with Polynucleotide Kinase Nick Translation Purification of labeled probe Random Primed labeling Techniques, overview Template Type of label Labeling of Oligonucleotides, see Labeling of DNA Labeling of RNA Choice of labeling method In vitro Transcription with RNA Polymerases LB medium, recipe Ligation of DNA LightCycler System 29 34 35 33 29 32 30 29 29 79 79 161 22 47
Liposomal and non-liposomal Transfection Reagents FuGENE HD Transfection Reagent X-tremeGENE siRNA Transfection Reagent Loading buffer for RNA gelelectrophoresis
127 127 127 155
M
M9 minimal medium, recipe MagNA Pure LC Instrument Magnesium chloride, recipe Mammalian cell: nucleic acid content Manipulation of DNA Manipulation of Proteins Manipulation of RNA Media for Bacteria Melting Curve Analysis (LightCycler) Melting temperatures, calculation of Metric prefixes MgCl2, recipe 161 8 149 119 2 82 61 161 57 164 165 149
179
Microinjection Molecular Weight Markers Molecular weight of DNA, calculation of via acrylamide and agarose gelelectrophoresis Molecular weight of Proteins, commonly used markers via denaturing SDS PAGE Molecular weight of RNA, calculation of via acrylamide and agarose gelelectrophoresis MOPS, recipe Mung Bean Nuclease, removing 3 and 5protruding ends of DNA Mycoplasma Contamination
130 10 3 11 92 92 63 69 149 26 115
N
NaCl, recipe NaOAc, general recipe recipe for buffer with desired pH Na phosphate, recipe for buffer with desired pH NH4OAc, recipe Nick Translation of DNA Nucleic Acid and Protein content of a bacterial cella Nucleic Acid content in a typical human cell Nucleic Acid content in human blood 149 149 152 153 148 33 119 119 120
P
PBS, recipe PCR Additives to reaction mix Choice of Polymerase Contamination, avoiding of Cycling profile initial denaturation denaturation during cycling final extension number of cycles primer annealing primer extension MgCl2 concentration Nucleotides concentration and storage pH of reaction mix PCR Standard Pipetting Scheme Expand High Fidelity Expand High Fidelity PLUS PCR System Expand Long Template PCR System FastStart Taq DNA Polymerase GC-Rich PCR System Taq, Pwo polymerase
151 42 41 36 43 43 44 44 43 43 40 41 42 44 41 41 41 41 41 41
180
Polymerase, concentration of product characteristics product selection Primers, annealing temperature concentration concentration via OD measurement conversion of g to pmol and pmol to g M to pmol and pmol to M design melting temperature molecular weight, calculation of Probe Designer Software (LightCycler) software storage PCR Real Time Analysis Real-Time PCR Assay Formats Fluorescence Resonance Energy Transfer Hybridization Probes HybProbe Format Melting Curve Analysis Probe Designer Software (LightCycler) Quantification Principles
42 41 41 38 38 39 39 39 40 38 39 51 40 38 46 48 50 48 50 59 51 55
PCR Template, amount, integrity and purity of Standard Temperature Profile for Taq, Tth and Pwo polymerase Periodical system of elements pH measurement Phenol, caution when using recipe Pipetting of DNA Pipetting of RNA pmol of ends of DNA, calculation of pmol of ends of RNA, calculation of Polynucleotide Kinase for 5end labeling of DNA and Oligonucleotides Ponceau S solution, recipe Potassium acetate, recipe for buffer with desired pH Potassium phosphate, recipe for buffer with desired pH Precautions for handling DNA Precautions for handling Proteins
37 45 168 147 156 156 2 62 3 63 35 159 152 153 2 82
181
Precautions for handling RNA Precipitation of Proteins with aceton ammonium sulfate chloroform/methanol Trichloroacetic acid Pressure, conversions Primers: Probe Designer Software (LightCycler System) Properties of Bacterial Cells Properties of Plant Cells Properties of Animal Cells Protease Activity, inhibition of Protease Inhibitor, product selection table Protector RNase Inhibitor Purification of antibodies via immunoprecipitation Purification of DNA: see Isolation of DNA Purification of Proteins via ion exchange chromatography via tagging Purification of RNA: see Isolation of RNA Purity of DNA via OD measurement Purity of RNA via OD measurement
60 97 96 97 97 167 51 117 118 118 83 85 61 107 109 111 9 68
Q
Quantification of Proteins: see concentration of Proteins
R
Radioisotopes: properties of Random primed labeling of DNA Rapid Translation System Real-Time PCR (see PCR Real Time Analysis) Remove 3and 5protruding ends of DNA Reporter Gene Assays CAT (Chloramphenicol Acetyltransferase) -Gal (-Galactosidase) Luc (Luciferase) hGH (Human Growth Hormon) SEAP (Secreted Human Placental Alkaline Phosphatase) GFP (Green Fluorescent Protein) Restriction Enzymes Activity in buffer system in PCR buffer mix Buffer system and components Characteristics of individual enzymes Inactivation Methylation, sensitivity to Partial Digest Pulse field gradient electrophoresis
166 32 103 24 142 144 143 143 143 143 143 15 15 12 15 14 15 21 14
182
Recognition sites Recognition sites, palindromic recognition sequences Removal from reaction mix Star activity Stability and storage Unit definition Reverse transcription of RNA: see RT-PCR RNAse Inhibitors RT-PCR Contamination, avoiding of One Step Procedures advantages description enzymes, choice of RT-PCR Polymerase, combinations with DNA polymerases divalention requirement RNase H Activity sensitivity and specificity temperature optima Primers for reverse transcription, choice of design of RNAse contamination, avoiding of
15 19 14 13 12 12 61 70 76 76 77 75 75 77, 78 75 75 71 72 70
Template, type and integrity Two Step Procedures advantages description enzymes, choice of RTS (see Rapid Translation System) Running buffer for Protein SDS PAGE
70 76 76 77 157
S
Sample buffer for DNA agarose gelelectrophoresis, recipe Protein SDS and urea PAGE RNA agarose gelelectrophoresis, recipe Selection Markers for Stabile Cell Lines Shrimp Alkaline Phosphatase for dephosphorylation SimpleProbe Format Size estimation of DNA via acryamide and agarose electrophoresis Size estimation of Proteins via denaturing SDS PAGE Size estimation of RNA via acrylamide and agarose electrophoresis SOB medium, recipe SOC medium, recipe Sodium acetate, general recipe recipe for buffer with desired pH
154 157 155 130 23 51 11 92 69 161 161 149 152
183
Sodium chloride, recipe Sodium dodecyl sulfate, recipe Sodium phosphate, recipe for buffer with desired pH SP6 Polymerase for labeling of RNA SSC, recipe SSPE, recipe Stabilization of Proteins Addition of osmolytes proteins salts reducing reagents specific ligands substrates Staining of Proteins on denaturing SDS PAGE gels Staining of Proteins on membranes Storage of DNA Storage of Proteins Storage of RNA Streptomycin, general information SYBR green staining for DNA and RNA gelelectrophoreis
149 150 153 80 151 151 86 86 86 87 87 87 93 93 2 82 61 160 156
T
T3 and T7 Polymerase for labeling of RNA TAE, recipe Tagging of Proteins TB medium, recipe TBE, recipe TBS, recipe TBST, recipe TCA, recipe TE, recipe Temperature, conversion between Centrigrade and Fahrenheit Temperature sensitivity of RNA Terminal transferase for 3end labeling of DNA and Oligonucleotides Tetracycline, general information Tissue culture reagents Fetal calf serum CO2 Incubator CO2 Incubator, concentrations Top agar overlay, recipe TPE, recipe
80 154 111 161 154 159 159 150 151 167 62 34 160 113 113 113 113 162 154
184
Transfection of mammalian cells Trichloroacetic acid, recipe Tris, general recipe recipe for buffer with desired pH
123 150 150 154
U
Universal ProbeLibrary 53
W
Western blotting, blocking solution, recipe transfer buffer for semi dry and wet blots, recipe 159 159
X
X-gal, recipe X-gal/IPTG indicator plates, recipe 150 162
Y
YT medium, recipe 161
Trademarks
COMPLETE, EXPAND, FASTSTART, HIGH PURE, LC, LIGHTCYCLER, LUMI-IMAGER, MAGNA PURE, NUTRIDOMA, RTS, SURE/CUT, TAQMAN, TITAN, TRIPURE, MINI QUICK SPIN, are trademarks of Roche. FuGENE is a registered trademark of Fugent, L.L.C., USA. UPL, PROBELIBRARY and LNA are trademarks of Exiqon A/S, Vedbaek, Denmark. Other brands or product names are trademarks of their respective holders.
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Great information compact format the RAS Lab FAQS, 3rd edition

Dear Valued Customer,

Table of contents (general overview):

Table of contents (general overview):

5. 5.1. 5.2. 5.3. 5.4.

145 146 160 161 163

Table of contents (detailed overview):

. . . . . . 36 . . . . . . .36 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .37 38 39 .40 40 41 41 .42 .42 .43 .44 .45

46 46 .47 48 49 50 54 .57 .57 59

Working with RNA . . . . . . . . . . . . . . . . . . . . 59

Working with Protein. . . . . . . . . . . . . . . . . . 81

. . . . . . . . . . .79 . . . . . . . . . . .80 . . . . . . . . . . .81

. . . .92 . . . . . . . . . . . . . . . . . . . . . . . . . . . .92 .93 .93 94 94 95 96 96 .97

Working with Cells . . . . . . . . . . . . . . . . . . 112

Preparing Buffers and Media . . . . . . . . . . 145

Conversion Tables and Formulars . . . . . . 163

Addresses and Index . . . . . . . . . . . . . . . . . 169

Working with DNA

1.1. 1.2. 1.3. 1.4. 1.5. 1.6. 1.7. 1.8. 1.9.

Precautions for handling DNA

Handling fresh and stored material before extraction of DNA

Manipulation of DNA Drying DNA

Working with DNA

Commonly used formulas

Molecular Weight of DNA, Calculation in Dalton*

e.g., MW of pBR322 dsDNA (4 363 basepairs)

= 4 363 x 660 Da = 2.9 x 10 6 Da = 2.9 x 103 kDa

MW of ssDNA = [number of bases] x [330 Da]

Calculation of pmol of 5 (or 3) ends

pmol of ends of a dsDNA molecule

e.g., pmol of 5or 3ends of 1 g of a 100 basepairs dsDNA fragment =

pmol of ends of a ssDNA molecule

e.g., pmol of 5or 3ends of 1 g of a 250 bases ssDNA fragment =

Working with DNA

Commonly used formulas

e.g., 1 g of a 100 basepairs dsDNA fragment =

pmol of ssDNA = g (of ssDNA) x

1 g (of ssDNA) x 3 030 10 6 pg 1 pmol x x = 1 g 330 pg Nb Nb 1 x 3 030 = 3.03 pmol 1 000

e.g., 1 g of a 1 000 bases ssDNA fragment =

g of dsDNA = pmol (of dsDNA) x

660 pg 1 g x x Nbp = 1 pmol 106 pg

g of ssDNA = pmol (of ssDNA) x

Working with DNA

Commonly used formulas

dsDNA fragment dsDNA fragment dsDNA fragment

* RE: restriction enzyme

Working with DNA

Isolating and purifying DNA

removal of unincorporated nucleotides from labeled DNA molecules

Working with DNA

Isolating and purifying DNA

DNA Isolation Kit for Cells and Tissues

Genopure Plasmid Midi Kit

Genopure Plasmid Maxi Kit

Working with DNA

Isolating and purifying DNA

Whole blood Cultured cells

White blood cells Tissues

Sizes and weights of DNA from different organism