L E A R N I N G

O B J E C T I V E S

&

S C I E N C E

C O M P E T E N C I E S

Application of the principles of DNA structure and genetic variation examined in this chapter will provide you with
the science competencies to be able to solve the following types of problems:
For a double-stranded DNA molecule, given the positions of cleavage sites for one or more restriction enzymes,
deduce the number and lengths of the fragments produced by cleaving the DNA with one or more of the enzymes,
and draw a diagram showing where these fragments would appear in a gel after electrophoresis.
Given the gel patterns of DNA fragments produced by cleavage of a double-stranded DNA molecule by each of
several restriction enzymes and combinations of these enzymes, infer the restriction map of the intact DNA
molecule that shows the positions of cleavage sites of the enzymes.
Shown the pattern of DNA bands in an electrophoresis gel used in DNA typing, identify which, if any, of a group
of individuals could be the source of the DNA.
Given the restriction map of a double-stranded DNA molecule and the region covered by a DNA or RNA probe,
specify which fragment or fragments of DNA would be labeled in a Southern blot using any one or more of the
restriction enzymes.
For a given sequence of DNA, select the sequences of primer oligonucleotides that would allow any specific fragment of the molecule to be amplified in the polymerase chain reaction.

ince the mid-1970s, studies in genetics

have undergone a revolution based on
the use of increasingly sophisticated
ways to isolate and identify specific fragments
of DNA. The culmination of these techniques
was large-scale genomic sequencingthe ability to determine the correct sequence of the
base pairs that make up the DNA in an entire
genome and to identify the sequences associated with genes. Because many of the laboratory organisms used in genetics experiments
have relatively small genomes, these sequences
were completed first. The techniques used to
sequence these simpler genomes were then
scaled up to sequence much larger genomes,
including the human genome.

2.1

Genetic Differences
Among Individuals

The human genome in a reproductive cell consists of approximately 3 billion base pairs organized into 23 distinct chromosomes (each
chromosome contains a single molecule of
duplex DNA). A typical chromosome can contain
several hundred to several thousand genes,
arranged in linear order along the DNA molecule
present in the chromosome. The sequences that
make up the protein-coding part of these genes
actually account for only about 1.3 percent of the
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CHAPTER 2

entire genome. The other 98.7 percent of the

sequences do not code for proteins. Some noncoding sequences are genetic chaff that gets
separated from the protein-coding wheat when
genes are transcribed and the RNA transcript is
processed into messenger RNA. Other noncoding
sequences are relatively short sequences that are
found in hundreds of thousands of copies scattered throughout the genome. Still other noncoding sequences are remnants of genes called
pseudogenes. As might be expected, identifying the
protein-coding genes from among the large background of noncoding DNA in the human genome
is a challenge in itself.
Geneticists often speak of the nucleotide
sequence of the human genome because corresponding DNA sequences from any two individuals are identical at about 99.9% of their
nucleotide sites. These shared sequences are our
evolutionary legacy; they contain the genetic
information that makes us human beings. In reality, however, there are many different human
genomes. Geneticists have great interest in the
0.1 percent of the human DNA sequence
3 million base pairsthat differs from one genome
to the next, because these differences include the
mutations that are responsible for genetic diseases
such as phenylketonuria and other inborn errors
of metabolism, as well as the mutations that
increase the risk of more complex diseases such as
heart disease, breast cancer, and diabetes.

DNA Structure and Genetic Variation

6/13/11 11:45 AM

Fortunately, only a small proportion of all

differences in DNA sequence are associated with
disease. Some of the others are associated with
inherited differences in height, weight, hair
color, eye color, facial features, and other traits.
Most of the genetic differences between people
are completely harmless. Many have no detectable effects on appearance or health. Such differences can be studied only through direct
examination of the DNA itself. These harmless
differences are nevertheless important, because
they serve as genetic markers.

individuals can serve as a genetic marker.

Although genetic markers are often harmless in
themselves, they allow the positions of disease
genes to be located along the chromosomes
and their DNA to be isolated, identified, and
studied.
Genetic markers that are detected by direct
analysis of the DNA are often called DNA markers. DNA markers are important in genetics
because they serve as landmarks in long DNA
molecules, such as those found in chromosomes,
which allow genetic differences among individuals to be tracked. They are like signposts along a
highway. Using DNA markers as landmarks, the
geneticist can identify the positions of normal
genes, mutant genes, breaks in chromosomes,
and other features important in genetic analysis
(FIGURE 2.1).
The detection of DNA markers usually
requires that the genomic DNA (the total
DNA extracted from cells of an organism) be
fragmented into pieces of manageable size

DNA Markers as Landmarks in Chromosomes

In genetics, a genetic marker is any difference in DNA, no matter how it is detected,
whose pattern of transmission from generation
to generation can be tracked. Each individual
who carries the marker also carries a length of
chromosome on either side of it, so that the
marker marks a particular region of the genome.
Any difference in DNA sequence between two

Chromosomes are located

in the cell nucleus.

Each chromosome contains

one long molecule of duplex
(double-stranded) DNA.

DNA markers are used

to identify particular
regions along the DNA
in chromosomes.
A

Nucleus

C
DNA marker
Double-stranded
DNA molecule

Chromosomes

Cleavage

HUMAN CELL
DNA fragment

Single DNA
fragments can
be cleaved from
the molecule.

BACTERIAL
CELL
CLONED DNA

Large quantities of the

cloned human DNA
fragment can be isolated
from the bacterial cells.

Replication in
bacterial cells

The fragments can be

transferred into bacterial
cells, where they can
replicate. (This is the
procedure of cloning.)

A DNA marker, in this case

D, serves to identify bacterial
cells containing a particular
DNA fragment of interest.

FIGURE 2.1 DNA markers serve as landmarks that identify physical positions along a DNA molecule, such as DNA from a chromosome. As shown above,
a DNA marker can also be used to identify bacterial cells into which a particular fragment of DNA has been introduced. The procedure of DNA cloning is
not quite as simple as indicated here; it is discussed further in Chapter 12.

2.1 Genetic Differences Among Individuals

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(usually a few thousand nucleotide pairs) that

can be manipulated in laboratory experiments.
In the following sections, we examine some of
the principal ways in which DNA is manipulated to reveal genetic differences among individuals, whether or not these differences find
outward expression. Use of these methods
broadens the scope of genetics, making it possible to carry out genetic analysis in any organism. This means that detailed genetic analysis is
no longer restricted to human beings, domesticated animals, cultivated plants, and the relatively small number of model organisms
favorable for genetic studies. Direct study of
DNA eliminates the need for prior identification
of genetic differences between individuals; it
even eliminates the need for controlled crosses.
The methods of molecular analysis discussed in
this chapter have transformed genetics:

holds the strands together. The complementary

strands also hold the key to replication, because
each strand can serve as a template for the synthesis of a new complementary strand. We will
now take a closer look at DNA structure and at
the key features of its replication.
Polynucleotide Chains
In terms of biochemistry, a DNA strand is a
polymera large molecule built from repeating
units. The units in DNA are composed of
2-deoxyribose (a five-carbon sugar), phosphoric acid, and the four nitrogen-containing
bases denoted A, T, G, and C. The chemical
structures of the bases are shown in FIGURE 2.2.
Note that two of the bases have a double-ring
structure; these are called purines. The other
two bases have a single-ring structure; these are
called pyrimidines.
The purine bases are adenine (A) and
guanine (G).
The pyrimidine bases are thymine (T)
and cytosine (C).
In DNA, each base is chemically linked to
one molecule of the sugar deoxyribose, forming a compound called a nucleoside. When a
phosphate group is also attached to the sugar,
the nucleoside becomes a nucleotide ( FIGURE2.3). Thus, a nucleotide is a nucleoside plus
a phosphate. In the conventional numbering
of the carbon atoms in the sugar in Figure 2.3,
the carbon atom to which the base is attached
is the 1 carbon. (The atoms in the sugar are
given primed numbers to distinguish them
from atoms in the bases.) The nomenclature of
the nucleoside and nucleotide derivatives of
the DNA bases is summarized in TABLE 2.1. Most
of these terms are not needed in this book;
they are included because they are likely to be
encountered in further reading.

The manipulation of DNA is the basic experimental operation in modern genetics.

The methods described in this chapter are the

principal techniques used in virtually every
modern genetics laboratory.

2.2 The Molecular Structure of DNA

Modern experimental methods for the manipulation and analysis of DNA grew out of a detailed
understanding of its molecular structure and replication. Therefore, to understand these methods,
one needs to know something about the molecular structure of DNA. We saw in Chapter 1 that
DNA is a helix of two paired, complementary
strands, each composed of an ordered string of
nucleotides, each bearing one of the bases A (adenine), T (thymine), G (guanine), or cytosine (C).
WatsonCrick base pairing between A and T and
between G and C in the complementary strands

Purines

Pyrimidines

Adenine
H

Cytosine

H
O

N
C

Thymine

Guanine

N1 6 5 C
2 A
C 3 4C
N

7
8
9

Deoxyribose

H
H

N
C

G
N

CH3
C
C

N
C

Deoxyribose

Deoxyribose

C6
N

C
5

T
2

C
O

4C
3

H
O
H

Deoxyribose

C
N

C
C

H
H

FIGURE 2.2 Chemical structures of the four nitrogen-containing bases in DNA: adenine, thymine, guanine, and cytosine. The nitrogen atom linked
to the deoxyribose sugar is indicated. The atoms shown in red participate in hydrogen bonding between the DNA base pairs.

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CHAPTER 2 DNA Structure and Genetic Variation

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oligonucleotide primers. To complete the cycle,

the temperature is raised slightly, to about 70C,
for the elongation of each primer. The steps of
denaturation, renaturation, and replication are
repeated from 2030 times, and in each cycle
the number of molecules of the amplified
sequence is doubled.
Implementation of PCR with conventional
DNA polymerases is not practical, because at
the high temperature necessary for denaturation, the polymerase is itself irreversibly
unfolded and becomes inactive. However, DNA
polymerase isolated from certain organisms is
heat stable because the organisms normally live
in hot springs at temperatures well above 90C,
such as are found in Yellowstone National Park.
Such organisms are said to be thermophiles.
The most widely used heat-stable DNA polymerase is called Taq polymerase, because it was
originally isolated from the thermophilic bacterium Thermus aquaticus.
PCR amplification is very useful for generating large quantities of a specific DNA sequence.
The principal limitation of the technique is that
the DNA sequences at the ends of the region to
be amplified must be known so that primer oligonucleotides can be synthesized. In addition,
sequences longer than about 5000 base pairs
cannot be replicated efficiently by conventional
PCR procedures, although there are modifications of PCR that allow longer fragments to be
amplified. On the other hand, many applications require amplification of relatively small
fragments. The major advantage of PCR amplification is that it requires only trace amounts of
template DNA. Theoretically only one template
molecule is required, but in practice the amplification of a single molecule may fail because the
molecule may, by chance, be broken or damaged. But amplification is usually reliable with
as few as 10100 template molecules, which
makes PCR amplification 10,000100,000 times
more sensitive than detection via nucleic acid
hybridization.
The exquisite sensitivity of PCR amplification has led to its use in DNA typing for criminal cases in which a minuscule amount of
biological material has been left behind by the
perpetrator (skin cells on a cigarette butt or
hair-root cells on a single hair can yield enough
template DNA for amplification). In research,
PCR is widely used in the study of independent
mutations in a gene whose sequence is known
in order to identify the molecular basis of each
mutation, to study DNA sequence variation
among alternative forms of a gene that may be
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CHAPTER 2

present in natural populations, or to examine

differences among genes with the same function in different species. The PCR procedure has
also come into widespread use in clinical laboratories for diagnosis. To take just one very
important example, the presence of the human
immunodeficiency virus (HIV), which causes
acquired immune deficiency syndrome (AIDS),
can be detected in trace quantities in blood
banks via PCR by using primers complementary
to sequences in the viral genetic material. These
and other applications of PCR are facilitated by
the fact that the procedure lends itself to automation by the use of mechanical robots to set
up and run the reactions.

2.5

The Terminology of Genetic

Analysis

In order to discuss the types of DNA markers

that modern geneticists commonly use in genetic
analysis, we must first introduce some key terms
that provide the essential vocabulary of genetics.
These terms can be understood with reference
to FIGURE 2.21. In Chapter 1 we defined a gene as
an element of heredity, transmitted from parents
to offspring in reproduction, that influences one
or more hereditary traits. Chemically, a gene is
a sequence of nucleotides along a DNA molecule. In a population of organisms, not all copies
of a gene may have exactly the same nucleotide
sequence. For example, whereas one form of a
gene may have the codon GCA at a certain position, another form of the same gene may have
the codon GCG. Both codons specify alanine.
Hence, the two forms of the gene encode the
same sequence of amino acids yet differ in DNA
sequence. The alternative forms of a gene are
called alleles of the gene. Different alleles may
also code for different amino acid sequences,
sometimes with drastic effects. Recall the example of the PAH gene for phenyalanine hydroxylase in Chapter 1, in which a change in codon
408 from CGG (arginine) to TGG (tryptophan)
results in an inactive enzyme that becomes
expressed as the inborn error of metabolism
phenylketonuria.
Within a cell, genes are arranged in linear
order along microscopic thread-like bodies called
chromosomes, which we will examine in detail
in Chapters 4 and 7. Each human reproductive
cell contains one complete set of 23 chromosomes containing 3  109 base pairs of DNA. A
typical chromosome contains several hundred to
several thousand genes. In humans the average
is approximately 1000 genes per chromosome.

DNA Structure and Genetic Variation

6/13/11 11:45 AM

Each chromosome contains a single molecule of

duplex DNA along its length, complexed with
proteins and very tightly coiled. The DNA in the
average human chromosome, when fully
extended, has relative dimensions comparable to
those of a wet spaghetti noodle 25 miles long;
when the DNA is coiled in the form of a chromosome, its physical compaction is comparable to
that of the same noodle coiled and packed into
an 18-foot canoe.
The physical position of a gene along a chromosome is called the locus of the gene. In most
higher organisms, including human beings, each
cell other than a sperm or egg contains two copies of each type of chromosomeone inherited
from the mother and one from the father. Each
member of such a pair of chromosomes is said to
be homologous to the other. (The chromosomes that determine sex are an important
exception, discussed in Chapter 4, which we will
ignore for now.) At any locus, therefore, each
individual carries two alleles, because one allele
is present at a corresponding position in each of
the homologous maternal and paternal chromosomes (Figure 2.21).
The genetic constitution of an individual is
called its genotype. For a particular gene, if the
two alleles at the locus in an individual are
indistinguishable from each other, then for this
gene the genotype of the individual is said to be
homozygous for the allele that is present. If
the two alleles at the locus are different from
each other, then for this gene the genotype of
the individual is said to be heterozygous for
the alleles that are present. Typographically,
genes are indicated in italics, and alleles are
typically distinguished by uppercase or lowercase letters (A versus a), subscripts (A1 versus
A2), superscripts (a versus a), or sometimes
just  and . Using these symbols, homozygous genes would be portrayed by any of these
formulas: AA, aa, A1A1, A2A2, aa, aa, ,
or . As in the last two examples, the slash
is sometimes used to separate alleles present in
homologous chromosomes to avoid ambiguity.
Heterozygous genes would be portrayed by any
of the formulas Aa, A1A2, aa, or . In Figure 2.21, the genotype Bb is heterozygous
because the B and b alleles are distinguishable
(which is why they are assigned different symbols), whereas the genotype CC is homozygous.
These genotypes could also be written as Bb
and CC, respectively.
Whereas the alleles that are present in an
individual constitute its genotype, the physical
or biochemical expression of the genotype is

Locus (physical position)

of gene A in each
homologous chromosome
Gene A

A1
A2
A3
A4
A5

Gene B

Gene C

Heterozygous
genotype Bb

Homozygous
genotype CC

Many different A
alleles can exist
in an entire population
of organisms, but only
a single allele can be
present at the locus of
the A gene in any one
chromosome.

Homologous
chromosomes

Genotypes are sometimes

written with a slash (for
example, B/b and C/C) to
distinguish the alleles in
homologous chromosomes.

FIGURE 2.21 Key concepts and terms used in modern genetics. Note that a single gene
can have any number of alleles in the population as a whole, but no more than two alleles
can be present in any one individual.

called the phenotype. To put it as simply as possible, the distinction is that the genotype of an
individual is what is on the inside (the alleles in
the DNA), whereas the phenotype is what is on
the outside (the observable traits, including biochemical traits, behavioral traits, and so forth).
The distinction between genotype and phenotype is critically important because there usually
is not a one-to-one correspondence between
genes and traits. Most complex traits, such as
hair color, skin color, height, weight, behavior,
life span, and susceptibility to disease, are influenced by many genes. Most traits are also influenced more or less strongly by environment.
This means that the same genotype can result in
different phenotypes, depending on the environment. Compare, for example, two people with a
genetic risk for lung cancer; if one smokes and
the other does not, the smoker is much more
likely to develop the disease. Environmental
effects also imply that the same phenotype can
result from more than one genotype; smoking
again provides an example, because most smokers who are not genetically at risk can also
develop lung cancer.

2.6

Types of DNA Markers

Present in Genomic DNA

Genetic variation, in the form of multiple

alleles of many genes, exists in most natural
populations of organisms. We have called such
genetic differences between individuals DNA
2.6

26105_CH02_039_078.pdf 63

One of each pair of

chromosomes is maternal in
origin, the other paternal.

Types of DNA Markers Present in Genomic DNA

63

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markers; they are also called DNA polymorphisms. (The term polymorphism literally
means multiple forms.) The methods of DNA
manipulation examined in Sections 2.3 and 2.4
can be used in a variety of combinations to
detect differences among individuals. Anyone
who reads the literature in modern genetics
will encounter a bewildering variety of acronyms referring to different ways in which
genetic polymorphisms are detected. The different approaches are in use because no single
method is ideal for all applications, each
method has its own advantages and limitations,
and new methods are continually being developed. In this section we examine some of the
principal methods for detecting DNA polymorphisms among individuals.
Single-Nucleotide Polymorphisms (SNPs)
A single-nucleotide polymorphism, or
SNP (pronounced snip), is present at a particular nucleotide site if the DNA molecules in
the population often differ in the identity of the
nucleotide pair that occupies the site. For example, some DNA molecules may have a TA base
pair at a particular nucleotide site, whereas other
DNA molecules in the same population may
have a CG base pair at the same site. This difference constitutes a SNP. The SNP defines two
alleles for which there could be three genotypes among individuals in the population:
homozygous with TA at the corresponding site
in both homologous chromosomes, homozygous with CG at the corresponding site in both
homologous chromosomes, or heterozygous
with TA in one chromosome and CG in the
homologous chromosome. The word allele is in
quotation marks above because the SNP need
not be in a coding sequence, or even in a gene.
In the human genome, any two randomly chosen DNA molecules are likely to differ at one
SNP site about every 1000 bp in noncoding DNA
and at about one SNP site every 3000 bp in
protein-coding DNA. Note, in the definition of a
SNP, the stipulation is that DNA molecules must
differ at the nucleotide site often. This provision excludes rare genetic variation of the sort
found in less than 1 percent of the DNA molecules in a population. The reason for the exclusion is that genetic variants that are too rare are
not generally as useful in genetic analysis as the
more common variants. SNPs are the most common form of genetic differences among people.
About 10 million SNPs have been identified that
are relatively common in the human population, and about 300,000600,000 of these are
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CHAPTER 2

typically used in a search for SNPs that might be

associated with complex diseases such as diabetes or high blood pressure.
Identifying the particular nucleotide present at each of a million SNPs is made possible
through the use of DNA microarrays containing millions of infinitesimal spots on a glass slide
about the size of a postage stamp. Each tiny spot
contains a unique DNA oligonucleotide
sequence present in millions of copies synthesized by microchemistry when the microarray
is manufactured. Each oligonucleotide sequence
is designed to hybridize specifically with small
fragments of genomic DNA that include one or
the other of the nucleotide pairs present in a
SNP. The microarrays also include numerous
controls for each hybridization. The controls
consist of oligonucleotides containing deliberate
mismatches that are intended to guard against
being misled by particular nucleotide sequences
that are particularly sticky and hybridize too
readily with genomic fragments and other
sequences that form structures that hybridize
poorly or not at all. Such microarrays, sometimes called SNP chips, enable the SNP genotype of an individual to be determined with
nearly 100 percent accuracy.
The principles behind oligonucleotide
hybridization are illustrated in FIGURE 2.22. Here
the length of each oligonucleotide is seven
nucleotides, but in practice this is too short.
Typical SNP chips consist of oligonucleotides at
least 25 nucleotides in length. Part A shows the
two types of DNA duplexes that might form a
SNP. In this example, some chromosomes carry
a DNA molecule with a TA base pair at the
position shown in red, whereas the DNA molecular in other chromosomes has a CG base pair
at the corresponding position. Short fragments
of genomic DNA are labeled with a fluorescent
tag and then the single strands hybridized with
a SNP chip containing the complementary oligonucleotides as well as the numerous controls.
The duplex containing the TA will hybridize
only with the two oligonucleotides on the left,
and that containing the CG will hybridize only
with the two oligonucleotides on the right.
After the hybridization takes place, the SNP
chip is examined with fluorescence microscopy
to detect the spots that fluoresce due to the tag
on the genomic DNA. The possible patterns are
shown in part B. Genomic DNA from an individual whose chromosomes contain two copies
of the TA form of the duplex (homozygous TA/
TA) will cause the two leftmost spots to fluoresce but the two rightmost spots will remain

DNA Structure and Genetic Variation

6/13/11 11:45 AM

In this example the SNP consists of a TA

base pair in some DNA duplexes and
a CG base pair in others.

(A)
Fragments of genomic
DNA are labeled with
a fluorescent molecule.

A C T G C AG
TGACGT C

Each oligonucleotide in
a SNP chip is attached
to a glass slide.

GC
AT
CG
GC
TA
CG
AT

Strands from
each duplex
will hybridize
only with their
complementary
oligonucleotides.

GC
AT
CG
GC
CG
CG
AT

TA
GC
AT
CG
GC
TA
CG

A C C G C AG
TGGCGT C

TA
GC
GC
CG
GC
TA
CG

(B)

Hybridization signal
from homozygous AT/AT
Hybridization signal
from heterozygous AT/CG
Hybridization signal
from homozygous CG/CG
FIGURE 2.22 (A) Oligonucleotides attached to a glass slide in a SNP chip can be used to identify duplex DNA molecules
containing alternative base pairs for a SNP, in this example a TA base pair versus a CG base pair. (B) The SNP genotype of an
individual can be determined by hybridization because DNA from genotypes that are homozygous TA/TA, homozygous CG/CG, or
heterozygous TA/CG each gives a different pattern of fluorescence.

unlabeled. Similarly, genomic DNA from a

homozygous CG/CG individual will cause the
two rightmost spots to fluoresce but not the two
on the left. Finally, genomic DNA from a heterozygous TA/CG individual will cause fluorescence of all four spots because the TA duplex
labels the two leftmost spots and the CG duplex
labels the two rightmost spots.
Use of SNP chips or other available technologies for high-throughput genotyping of
millions of SNPs in thousands of individuals
allows genetic risk factors for disease to be identified. A typical study compares the genotypes
of patients with particular diseases with healthy
people matched with the patients for such factors as sex, age, and ethnic group. Comparing
the SNP genotypes among these groups often
reveals which SNPs in the genome mark the
location of the genetic risk factors, as will be
explained in greater detail in Section 2.7.

Restriction Fragment Length

Polymorphisms (RFLPs)
Although most SNPs require DNA sequencing to be studied, those that happen to be
located within a restriction site can be analyzed
in another way. An example of this situation
is shown in FIGURE 2.23, where the SNP consists
of a TA nucleotide pair in some molecules
and a CG pair in others. In this example, the
polymorphic nucleotide site is included in a
cleavage site for the restriction enzyme EcoRI
(5-GAATTC-3). The two nearest flanking EcoRI
sites are also shown. In this kind of situation,
DNA molecules with TA at the SNP will be
cleaved at both flanking sites and also at the
middle site, yielding two EcoRI restriction fragments. Alternatively, DNA molecules with CG
at the SNP will be cleaved at both flanking sites
but not at the middle site (because the presence
of CG destroys the EcoRI restriction site) and so
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Types of DNA Markers Present in Genomic DNA

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connection
Origin of the Human Genetic Linkage Map
This historic paper stimulated a
major international effort to establish
a genetic linkDavid Botstein,1
age map of the
Raymond L. White,2 Mark human genome
Skolnick,3 and Ronald W. based on DNA
Davis4 1980
polymorphisms.
1
Massachusetts Institute of
Pedigree studies
Technology, Cambridge,
using these
Massachusetts
genetic markers
2
University of Massachusetts
soon led to the
Medical Center, Worcester,
chromosomal
Massachusetts
localization and
3
University of Utah, Salt Lake
identification of
City, Utah
mutant genes
4
Stanford University, Stanford, for hundreds of
California
human disConstruction of a Genetic
eases. A more
Linkage Map in Man Using
ambitious goal,
Restriction Fragment Length
still only partly
Polymorphisms
achieved, is to
understand the
genetic and environmental interactions
involved in complex traits such as heart
disease and cancer. The small set of
large pedigrees called for in the excerpt
was soon established by the Centre
dEtude du Polymorphisme Humain
(CEPH) in Paris, France, and made
available to investigators worldwide
for genetic linkage studies. Today the
CEPH maintains a database on the

(A)
GAAT TC
CT TAAG

individuals in these pedigrees that com- segregating in a pedigree to be

prises approximately 15,000 polymor- mapped. Such a procedure would
phic DNA markers and 3 million not require any knowledge of the
genotypes.
biochemical nature of the trait or of
No method of systematically the nature of the alterations in the
mapping human genes has been DNA responsible for the trait. . . . The
devised, largely because of the pau- most efficient procedure will be to
city of highly polymorphic marker study a small set of large pedigrees
loci. The advent of recombinant DNA which have been genotyped for all
technology has suggested a theoreti- known polymorphic markers. . . .
cally possible way to define an arbi- The resolution of genetic and envitrarily large number of
ronmental components
arbitrarily polymorphic
of disease . . . must
In principle, linked
marker loci. . . . A subinvolve unraveling the
marker loci can allow
set of such polymorunderlying genetic
one to establish, with
phisms can readily be
predisposition, underhigh certainty, the
detected as differenstanding the environgenotype of an
ces in the length of
mental contributions,
individual.
DNA fragments after
and understanding the
digestion with DNA
variability of expression
sequence-specific restriction endo- of the phenotype. In principle, linked
nucleases. These restriction fragment marker loci can allow one to eslength polymorphisms (RFLPs) can tablish, with high certainty, the
be easily assayed in individuals, facil- genotype of an individual and, conitating large population studies. . . . sequently, assess much more pre[Genetic mapping] of many DNA cisely the contribution of modifying
marker loci should allow the estab- factors such as secondary genes, likelishment of a set of well-spaced, lihood of expression of the phenohighly polymorphic genetic markers type, and environment.
covering the entire human genome
[and enabling] any trait caused Source: D. Botstein, et al., Am. J. Hum. Genet.
wholly or partially by a major locus 32(1980): 314331.

Polymorphic
G A A T T C site
GAAT TC
CT TAAG
CT TAAG

5
3

3
5
Treatment of DNA
with EcoRI

(B)
GAAT TC
CT TAAG

Polymorphic
G A A C T C site
GAAT TC
CT TGAG
CT TAAG

5
3

3
5
Treatment of DNA
with EcoRI
No cleavage

Cleavage
Result: Two fragments

Result: One larger fragment

FIGURE 2.23 A difference in the DNA sequence of two molecules can be detected if the difference eliminates a restriction site. (A) This molecule
contains three restriction sites for EcoRI, including one at each end. It is cleaved into two fragments by the enzyme. (B) This molecule has an
altered EcoRI site in the middle, in which 5-GAATTC-3 becomes 5-GAACTC-3. The altered site cannot be cleaved by EcoRI, so treatment of
this molecule with EcoRI results in one larger fragment.

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will yield only one larger restriction fragment. A

SNP that eliminates a restriction site is known as
a restriction fragment length polymorphism, or RFLP (pronounced either as riflip
or by spelling it out).
Because RFLPs change the number and size
of DNA fragments produced by digestion with a
restriction enzyme, they can be detected by the
Southern blotting procedure discussed in Section 2.3. An example appears in FIGURE 2.24. In
this case the labeled probe DNA hybridizes near
the restriction site at the far left and identifies
the position of this restriction fragment in the
electrophoresis gel. The duplex molecule labeled
allele A has a restriction site in the middle
and, when cleaved and subjected to electropho-

resis, yields a small band that contains sequences

homologous to the probe DNA. The duplex
molecule labeled allele a lacks the middle
restriction site and yields a larger band. In this
situation there can be three genotypesAA, Aa,
or aa, depending on which alleles are present in
the homologous chromosomesand all three
genotypes can be distinguished as shown in the
Figure 2.24. Homozygous AA yields only a small
fragment, homozygous aa yields only a large
fragment, and heterozygous Aa yields both a
small and a large fragment. Because the presence of both the A and a alleles can be detected
in heterozygous Aa genotypes, A and a are said
to be codominant. In Figure 2.24, the bands
from AA and aa have been shown as somewhat

Positions of
cleavage sites
Direction of current
Site of hybridization
with probe DNA
Allele A

Larger DNA
fragments

5
3

Smaller DNA
fragments

3
5
Duplex DNA

FIGURE 2.24 In a restriction fragment length

polymorphism (RFLP), alleles may differ in the
presence or absence of a cleavage site in the
DNA. In this example, the a allele lacks a
restriction site that is present in the DNA of the
A allele. The difference in fragment length can
be detected by Southern blotting. RFLP alleles
are codominant, which means that DNA from
the heterozygous Aa genotype yields each of
the single bands observed in DNA from
homozygous AA and aa genotypes.

DNA band
from allele A

Allele a

5
3

3
5
Duplex DNA
DNA band
from allele a
Duplex DNA in homologous
chromosomes

5
3

3
5

5
3

3
5

5
3

3
5

5
3

3
5

5
3

3
5

5
3

3
5

Homozygous AA
DNA band
from genotype AA

Heterozygous Aa
DNA bands
from genotype Aa

Homozygous aa
DNA band
from genotype aa

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thicker than those from Aa, because each AA

genotype has two copies of the A allele and each
aa genotype has two copies of the a allele, compared with only one copy of each allele in the
heterozygous genotype Aa.

number of copies of the tandem repeat, typically

ranging from ten to a few hundred. FIGURE 2.25
illustrates DNA molecules that differ in the number of tandem repeats. In this case the number of
repeats varies from 1 to 10. When any of the
DNA molecules is cleaved with a restriction
endonuclease that cleaves at sites flanking the
tandem repeat, the size of the resulting restriction fragment is determined by the number of
repeats that it contains. A molecule of duplex
DNA containing the repeats can also be amplified
by means of the polymerase chain reaction (PCR)

Tandem Repeat Polymorphisms

An important type of DNA polymorphism
results from differences in the number of copies
of a DNA sequence that may be repeated many
times in tandem at a particular site in a chromosome. Any particular chromosome may have any

Direction of current
Positions of cleavage sites

Larger DNA
fragments
Duplex DNA
molecules

1
5
3

3
5
1

Position
of band in
DNA gel

5
3

3
5
1

Smaller DNA
fragments

5
3

3
5
1

5
3

3
5
1

5
3

3
5
1

5
3

3
5
1

5
3

3
5
1

5
3

3
5
1

5
3

3
5
1

10

5
3

3
5
Tandem repeats of a DNA sequence

FIGURE 2.25 A genetic polymorphism in which the alleles in a population differ in the number of copies of a DNA sequence (typically 260 bp)
that is repeated in tandem along the chromosome. This example shows alleles in which the repeat number varies from 1 to 10. Cleavage at
restriction sites flanking the repeat yields a unique fragment length for each allele. The alleles can also be distinguished by the size of the fragment
amplified by PCR using primers that flank the repeat.

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using primers flanking the tandem repeat.

Whether obtained by endonuclease digestion or
PCR, the resulting DNA fragments increase in
size according to the number of repeats they contain. Therefore, as shown at the right in Figure 2.25, two DNA molecules that differ in the
number of copies of the tandem repeat can be
distinguished because each will produce a different sized DNA fragment that can be separated by
means of electrophoresis.
The acronym SSR stands for simple
sequence repeat. An example of an SSR is the
repeating sequence 5-ACACACAC-3. Two
reasons make SSRs important in human genetic
analysis:
1. SSRs are abundant in the human genome.
2. SSRs are often highly polymorphic in
human populations.
As to their abundance in the human genome,
the most common SSRs are tabulated in
TABLE 2.4. There are many more dinucleotide
repeats than trinucleotide repeats, but there are
great differences in abundance within each class.
The most common dinucleotide repeat is 5-
ACACACAC-3, which is present at more
than 80,000 locations throughout the human
genome. On average, the human genome has
one SSR every 2 kb of human DNA, or about
1.5 million SSRs altogether.
The tendency of SSRs to be polymorphic in
copy number makes them very useful as genetic
markers. The typical SSR has a repeat length of

Table 2.4

Some simple sequence repeats in the

human genome

SSR repeat unit

5-AC-3
5-AT-3
5-AG-3
5-GC-3
5-AAT-3
5-AAC-3
5-AGG-3
5-AAG-3
5-ATG-3
5-CGG-3
5-ACC-3
5-AGC-3
5-ACT-3

Number of SSRs in
the human genome
80,330
56,260
23,780
290
11,890
7,540
4,350
4,060
2,030
1,740
1,160
870
580

Source: Data from International Human Genome

Sequencing Consortium, Nature 409(2001): 860921.

29 nucleotides. A polymorphism in the number

of repeats when the repeating unit is longer (in
the range 1060 nucleotides) is called a variable
number of tandem repeats (VNTR). Because
the repeat unit is longer in VNTRs, DNA fragments that differ in the number of copies are
more easily distinguished in electrophoresis gels
than are restriction fragments from SSRs (Figure 2.25). For this reason VNTRs have been useful in DNA typing (sometimes called DNA
fingerprinting) for individual identification
and for assessing the degree of genetic relatedness between individuals.
Not only do tandem repeats of DNA
sequences tend to be polymorphic, but most
polymorphisms tend to have a large number of
alleles. Each allele corresponds to a DNA molecule with a different number of copies of the
repeating unit, as illustrated in Figure 2.25. In
other words, a polymorphism in the number of
tandem repeats usually has multiple alleles in
the population. Even with multiple alleles, however, any particular chromosome must carry only
one of the alleles defined by the number of tandem repeats, and any individual genotype can
carry at most two different alleles. Nevertheless,
a large number of alleles implies an even larger
number of genotypes. For example, even with
only 10 alleles in a population, there could be 10
different homozygous genotypes and 45 different
heterozygous genotypes.
More generally, with n alleles there are a
total of n(n  1)/2 possible genotypes of which
n are homozygous and n(n  1)/2 are heterozygous. Consequently, if an SSRP or VNTR has a
relatively large number of alleles in a population, but no one allele is exceptionally common,
then each of the many genotypes in the population will have a relatively low frequency. If the
genotypes at 68 highly polymorphic loci are
considered simultaneously, then each possible
multiple-locus genotype is exceedingly rare.
The very low frequency of any multiple-locus
genotype is what gives tandem-repeat polymorphisms their utility in DNA typing. The use of
DNA typing in criminal investigation is exemplified in Problems 2.29 and Challenge Problem 2
at the end of this chapter and discussed further
in Chapter 17.
Copy-Number Variation (CNV)
In addition to the small-scale variation in
copy number represented by such genomic features as tandem repeats of short sequences (SSRs
and VNTRs), a substantial portion of the human
genome can be duplicated or deleted in much
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larger but still submicroscopic chunks ranging

from 1 kb to 1 Mb (Mb stands for megabase pairs,
or one million base pairs). This type of variation
is known as copy-number variation or CNV.
The extra or missing copies of the genome in
CNVs can be detected by means of hybridization
with oligonucleotides in DNA microarrays.
Because each spot on the microarray consists of
millions of identical copies of a particular oligonucleotide sequence, the number of these that
undergo hybridization depends on how many
copies of the complementary sequence are present in genomic DNA. A typical region is present
in two copies (one inherited from the mother
and the other from the father). If an individual
has an extra copy of the region, the ratio of
hybridization and therefore fluorescence intensity will be 32, whereas if an individual has a
missing copy, the ratio of hybridization and
therefore fluorescence intensity will be 12.
These differences can readily be detected with
DNA microarrays. Moreoever, because CNVs are
relatively large, a microarray typically will have
many different oligonucleotides that are complementary to sequences at intervals across the
CNV; hence, the CNV will result in a increase or
decrease in signal intensity of all the oligonucleotides included in the CNV. Current SNP chips
also include about a million oligonucleotide
probes designed to detect known CNVs.
CNVs by definition exceed 1 kb in size, but
many are much larger. In one study of about 300
individuals with their ancestry in Africa, Europe,
or Asia, approximately 1500 CNVs were discovered by hybridization with microarrays. These
averaged 200300 kb in length. In the aggregate,
the CNVs included 300450 million base pairs, or
1015 percent of the nucleotides in the entire
genome. Many of the CNVs were located in
regions near known mutant genes associated
with hereditary diseases. CNVs in alpha and beta
hemoglobin genes are known to be associated
with resistance to malaria, and CNVs in an HIV-1
receptor gene CCL3 are associated with resistance
to AIDS. The prevalence of CNVs has prompted
the inclusion of CNV oligonucleotides onto DNA
microarrays in order to be able to assess what
effects CNVs may have on the risk of complex
diseases such as diabetes or Alzheimer disease.

2.7

Applications of DNA Markers

Why are geneticists interested in DNA markers

and DNA polymorphisms? Their interest can be
justified on any number of grounds. In this section we consider the reasons most often cited.
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Genetic Markers, Genetic Mapping,

and Disease Genes
Perhaps the key goal in studying DNA polymorphisms in human genetics is to identify the
chromosomal location of mutant genes associated with hereditary diseases. In the context of
disorders caused by the interaction of multiple
genetic and environmental factors, such as
heart disease, cancer, diabetes, depression, and
so forth, it is important to think of a harmful
allele as a risk factor for the disease, which
increases the probability of occurrence of the
disease, rather than as a sole causative agent.
This needs to be emphasized, especially because
genetic risk factors are often called disease
genes. For example, the major disease gene
for breast cancer in women is the gene BRCA1.
For women who carry a mutant allele of
BRCA1, the lifetime risk of breast cancer is about
36 percent, and hence most women with this
genetic risk factor do not develop breast cancer.
On the other hand, among women who are not
carriers, the lifetime risk of breast cancer is
about 12 percent, and hence many women
without the genetic risk factor do develop breast
cancer. Indeed, BRCA1 mutations are found in
only 16 percent of affected women who have a
family history of breast cancer. The importance
of a genetic risk factor can be expressed quantitatively as the relative risk, which equals the
ratio of affected : nonaffected among persons
who carry the risk factor divided by the ratio of
affected : nonaffected among those who do not
carry it. In the case of BRCA1, the relative risk is,
therefore, 0.36/0.64  0.562 divided by
0.12/0.88  0.136, which equals 4.1.
The utility of DNA polymorphisms in locating and identifying disease genes results from
genetic linkage, the tendency for genes that
are sufficiently close together in a chromosome
to be inherited together. Genetic linkage will be
discussed in detail in Chapter 5, but the key concepts are summarized in FIGURE 2.26, which shows
the location of many DNA polymorphisms along
a chromosome that also carries a genetic risk factor denoted D (for disease gene). Each DNA polymorphism serves as a genetic marker for its own
location in the chromosome. The importance of
genetic linkage is that DNA markers that are sufficiently close to the disease gene will tend to
be inherited together with the disease gene in
pedigreesand the closer the markers, the stronger this association. Hence, the initial approach
to the identification of a disease gene is to find
DNA markers that are genetically linked with the
disease gene in order to identify its chromosomal

DNA Structure and Genetic Variation

6/13/11 11:45 AM

Locus of a disease gene

(a genetic risk factor), D

DNA markers that are too far from the

disease gene in the chromosome (or are in a
different chromosome) are not linked to the
disease gene. They do not tend to be
inherited with the disease gene in pedigrees.

DNA markers that are close enough

to a disease gene tend to be inherited
together (genetically linked) with the
disease gene.
D

DNA polymorphisms
(genetic markers) along
the chromosomes

The closer a marker is to the disease gene,

the closer the linkage and the more
likely it is that they will be inherited together.

FIGURE 2.26 Concepts in genetic localization of genetic risk factors for disease. Polymorphic DNA markers (indicated by the
vertical lines) that are close to a genetic risk factor (D) in the chromosome tend to be inherited together with the disease itself. The
genomic location of the risk factor is determined by examining the known genomic locations of the DNA polymorphisms that are
linked with it.

location, a procedure known as genetic mapping. Once the chromosomal position is known,
other methods can be used to pinpoint the
disease gene itself and to study its functions.
If genetic linkage seems a roundabout way to
identify disease genes, consider the alternative.
The human genome contains approximately
30,000 genes. If genetic linkage did not exist, then
we would have to examine 30,000 DNA polymorphisms, one in each gene, in order to identify
a disease gene. But the human genome has only
23 pairs of chromosomes, and because of genetic
linkage and the power of genetic mapping, it
actually requires only a few hundred DNA polymorphisms to identify the chromosome and
approximate location of a genetic risk factor.
Other Uses for DNA Markers
DNA polymorphisms are widely used in all
aspects of modern genetics because they provide a large number of easily accessed genetic
markers for genetic mapping and other purposes. Among the other uses of DNA polymorphisms are the following.
Individual identification. We have
already mentioned that DNA polymorphisms
have application as a means of DNA typing
(DNA fingerprinting) to identify different
individuals in a population. DNA typing in
other organisms is used to determine individual animals in endangered species and to
identify the degree of genetic relatedness
among individual organisms that live in
packs or herds. For example, DNA typing in
wild horses has shown that the wild stallion
in charge of a harem of mares actually sires
fewer than one-third of the foals.

Epidemiology and food safety science.

DNA typing also has important applications in
tracking the spread of viral and bacterial epidemic diseases, as well as in identifying the
source of contamination in contaminated foods.
Human population history. DNA polymorphisms provide important information in
anthropology to reconstruct the evolutionary
origin, global expansion, and diversification
of the human population.
Improvement of domesticated plants
and animals. Plant and animal breeders
have turned to DNA polymorphisms as
genetic markers in pedigree studies to identify, by genetic mapping, genes that are associated with favorable traits in order to
incorporate these genes into currently used
varieties of plants and breeds of animals.
History of domestication. Plant and animal breeders also study genetic polymorphisms to identify the wild ancestors of
cultivated plants and domesticated animals,
as well as to infer the practices of artificial
selection that led to genetic changes in these
species during domestication.
DNA polymorphisms as ecological indicators. DNA polymorphisms are being evaluated as biological indicators of genetic
diversity in key indicator species present in
biological communities exposed to chemical,
biological, or physical stress. They are also
used to monitor genetic diversity in endangered species and species bred in captivity.
Evolutionary genetics. DNA polymorphisms are studied in an effort to describe the
2.7 Applications of DNA Markers

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patterns in which different types of genetic

variation occur throughout the genome, to
infer the evolutionary mechanisms by which
genetic variation is maintained, and to illuminate the processes by which genetic polymorphisms within species become transformed
into genetic differences between species.
Population studies. Population ecologists
employ DNA polymorphisms to assess the
level of genetic variation in diverse populations of organisms that differ in genetic organization (prokaryotes, eukaryotes, organelles),
population size, breeding structure, or life-

history characters, and they use genetic polymorphisms within subpopulations of a species
as indicators of population history, patterns of
migration, and so forth.
Evolutionary relationships among species. Differences in DNA sequences between
species is the basis of molecular phylogenetics,
in which the sequences are analyzed to
determine the ancestral history (phylogeny)
of the species and to trace the origin of morphological, behavioral, and other types of
adaptations that have arisen in the course of
evolution.

A DNA strand is a polymer of A,

T, G and C deoxyribonucleotides
joined 3-to-5 by phosphodiester
bonds.
The two DNA strands in a duplex
are held together by hydrogen
bonding between the AT and
GC base pairs and by base
stacking of the paired bases.
Each type of restriction endonuclease enzyme cleaves doublestranded DNA at a particular
sequence of bases usually four or
six nucleotides in length.

The DNA fragments produced by

a restriction enzyme can be
separated by electrophoresis,
isolated, sequenced, and manipulated in other ways.
Separated strands of DNA or RNA
that are complementary in
nucleotide sequence can come
together (hybridize) spontaneously to form duplexes.
DNA replication takes place only
by elongation of the growing
strand in the 5-to-3 direction
through the addition of successive nucleotides to the 3 end.

In the polymerase chain reaction,

short oligonucleotide primers are
used in successive cycles of DNA
replication to amplify selectively a
particular region of a DNA duplex.
Genetic markers in DNA provide
a large number of easily accessed
sites in the genome that can be
used to identify the chromosomal
locations of disease genes, for
DNA typing in individual identification, for the genetic improvement of cultivated plants and
domesticated animals, and for
many other applications.

What four bases are commonly found in the

nucleotides in DNA? Which form base pairs?

What are restriction enzymes and why are

they important in the study of particular
DNA fragments? What does it mean to say
that most restriction sites are palindromes?

in advance? What is the role of the

oligonucleotide primers?

Which chemical groups are present at the

extreme 3 and 5 ends of a single polynucleotide strand?
What does it mean to say that a single
strand of DNA strand has a polarity? What
does it mean to say that the DNA strands in
a duplex molecule are antiparallel?

Describe how a Southern blot is carried out.

Explain what it is used for. What is the role
of the probe?
How does the polymerase chain reaction
work? What is it used for? What information
about the target sequence must be known

What is a DNA marker? Explain how

harmless DNA markers can serve as aids in
identifying disease genes through genetic
mapping.
Define and given an example of each of the
following key genetic terms: locus, allele,
genotype, heterozygous, homozygous,
phenotype.

Draw a diagram of the linear DNA showing the relative positions of the MluI and HindIII sites and the
distances in kb between them.
(b) A probe labeled with 32P made from one of the bacteriophage genes hybridizes with the 5 kb fragment
from the MluI digest and the 3 kb and 15 kb fragments
from the HindIII digest.
(a)

Linear double-stranded DNA from a bacteriophage is isolated, labeled at both 5 ends with 32P, and
digested with restriction enzymes. MluI produces fragments of 5, 7, and 13 kb. A Southern blot of this digest
shows the radioactive label in the bands at 5 and 7 kb.
HindIII cleaves the same molecule into 3, 7, and 15 kb fragments, and in this case the 3 and 7 kb bands contain the
32
P. Digestion with both enzymes produces fragments of
sizes 2, 3, 4, 5, and 11 kb.
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Show the approximate location of the gene on the

restriction map.

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(c)
(d)

B7, assuming that B3  Any purine.

B8, assuming that B4  A or T.

where the arrow denotes the site of cleavage in each

strand. If the resulting fragments were brought
together in the same order as in the original duplex
and the breaks in the backbones sealed, what possible DNA duplexes would be expected?

OH

1 P

B1 B5

2 P

B2 B6

3 P

B3 B7

4 P

B4 B8

5-CTGGGGCGCCCTCGTCAGCGAGGGGGCGCCGAT-3
3-GACCCCGCGGGAGCAGTCGCTCCCCCGCGGCTA-5
2.17

The restriction enzymes PstI, PvuII, and MluI have the

following restriction sites, where the arrow indicates
the site of cleavage in each strand:
PstI
5-CTGCAG-3
PvuII
5-CAGCTG-3
MluI
5-ACGCGT-3
A DNA duplex with the following sequence is digested

5-ATGCCCTGCAGTACCATGACGCGTTACGCAGCTGATCGAAACGCGTATATATGCC-3

HO

2.11

2.12

2.13

2.14

2.15

2.16

In the precursor nucleotides of the DNA duplex diagrammed in Problem 2.10, with which base was
each of the phosphate groups 14 associated with
prior to its incorporation into the polynucleotide
strand?
In a random sequence consisting of equal proportions
of all four nucleotides, what is the probability that a
particular short sequence of nucleotides matches a
restriction site for:
(a) A restriction enzyme with a 4-base cleavage
site?
(b) A restriction enzyme with a 6-base cleavage
site?
(c) A restriction enzyme with an 8-base cleavage site?
In a random sequence consisting of equal proportions
of all four nucleotides, what is the average distance
between restriction sites for:
(a) A restriction enzyme with a 4-base cleavage
site?
(b) A restriction enzyme with a 6-base cleavage
site?
(c) A restriction enzyme with an 8-base cleavage site?
If Escherichia coli DNA were essentially a random
sequence of 4.6  106 bp with equal proportions of
all four nucleotides (this is an oversimplification),
approximately how many restriction fragments
would be expected from cleavage with
(a) A 4-cutter restriction enzyme?
(b) A 6-cutter restriction enzyme?
(c) An 8-cutter restriction enzyme?
Consider the restriction enzymes AsiSI (cleavage
site 5-GCGATCGC-3) and BsiEI (cleavage site
5-CGATCG-3), where the downward arrow denotes
the site of cleavage in each strand. Is every AsiSI site a
BsiEI site? Is every BsiEI site a AsiSI site? Explain your
answer.
A DNA duplex with the sequence shown below is
cleaved with KasI (cleavage site 5-GGCGCC-3),

3-TACGGGACGTCATGGTACTGCGCAATGCGTCGACTAGCTTTGCGCATATATACGG-5

What fragments would result from cleavage with:

(a) PstI?
(b) PvuII?
(c) MluI?
2.18 Consider the sequence:
5-CTGCAGGTG-3
3-GACGTCCAC-5

If this sequence were cleaved with PstI

(5-CTGCAG-3), could it still be cleaved with PvuII
(5-CAGCTG-3)? If it were cleaved with PvuII, could
it still be cleaved with PstI? Explain your answer.
2.19 A circular DNA molecule is cleaved with AfeI, NheI,
or both restriction enzymes together. The accompanying diagram shows the resulting electrophoresis
gel, with the band sizes indicated. Draw a diagram of
the circular DNA showing the relative positions of
the AfeI and NheI sites.

AfeI

NheI

4 kb
3 kb
1 kb

2.20 In the diagrams of DNA fragments shown here, the

tick marks indicate the positions of restriction sites

for a particular restriction enzyme. A mixture of the
two types of molecules is digested and analyzed
with a Southern blot using either probe A or probe
B, which hybridize to the fragments at the positions
shown by the rectangles. In the accompanying
gel diagram, indicate the bands that would result
from each of these probes. (The scale on the right

Analysis and Applications

26105_CH02_039_078.pdf 75

AfeI
+
NheI

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ANALYSIS

AND

APPLICATI O N S ,

C O N T.

shows the expected positions of fragments from

112 kb.)
4 kb

6 kb

A1

8 kb

4 kb
10 kb

A2
12 kb
Probe A
Probe A

12 kb
9 kb

Probe B
Probe B

6 kb
12 kb
9 kb

3 kb

6 kb

1 kb

3 kb

2.23 The thick horizontal lines shown here represent

1 kb

2.21 In the accompanying diagram, the tick marks indicate

the positions of restriction sites in two alternative DNA

fragments that can be present at the a locus in a
human chromosome. An RFLP analysis is carried out,
using probe DNA that hybridizes with the fragments
at the position shown by the rectangle. With respect
to this RFLP, how many genotypes are possible? (Use
the symbol A1 to refer to the allele that yields the
upper DNA fragment, and A2 to refer to the allele that
yields the lower DNA fragment.) In the accompanying
gel diagram, indicate the genotypes across the top and
the phenotype (band position or positions) expected
of each genotype. (The scale on the right shows the
expected positions of fragments from 112 kb.)

A1
A2

4 kb

3 kb
7 kb

12 kb
9 kb
6 kb
3 kb
1 kb

alternative DNA molecules at a particular locus in

a human chromosome. The tick marks indicate the
positions of restriction sites for a particular restriction enzyme. Genomic DNA from a sample of people is digested and analyzed by a Southern blot
using a probe DNA that hybridizes at the position
shown by the rectangle. How many possible RFLP
alleles would be observed in the sample? How
many genotypes?
3 kb

3 kb

3 kb

2 kb

4 kb

5 kb
6 kb

4 kb
2 kb

4 kb

2.24 The RFLP described in Problem 2.23 is analyzed

with the same restriction enzyme but a different

probe, which hybridizes at the site indicated here by
the rectangle. How many RFLP alleles would be
found in this case? How many genotypes? (Use the
symbols A1, A2, etc. to indicate the alleles.) In the
accompanying gel diagram, indicate the genotypes
across the top and the phenotype (band position or
positions) expected of each genotype. (The scale on
the right shows the expected positions of fragments
from 112 kb.)
3 kb

3 kb

3 kb

2 kb

5 kb
6 kb

4 kb
4 kb

2 kb

4 kb

2.22 The accompanying diagram shows the DNA fragments

associated with an RFLP in the human genome

revealed by a probe that hybridizes at the position
shown by the rectangle. The tick marks are cleavage
sites for the restriction enzyme used in the RFLP analysis. How many alleles would this restriction enzyme
and this probe detect? How many genotypes would be
possible? In the accompanying gel diagram, indicate
the phenotype (pattern of bands) expected of each
genotype. (The scale on the right shows the expected
positions of fragments from 112 kb.)
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12 kb
9 kb
6 kb
3 kb
1 kb

CHAPTER 2 DNA Structure and Genetic Variation

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2.25

If pentamers were long enough to serve as specific

oligonucleotide primers for PCR (in practice they are
too short), what DNA fragment would be amplified
using the forward primer 5-AATGC-3 and the
reverse primer 3-GCATG-5 acting on the doublestranded DNA molecule shown here?

Locus 1

5-GATTACCGGTAAATGCCGGATTAACCCGGGTTATCAGGCCACGTACAACTGGAGTCC-3
3-CTAATGGCCATTTACGGCCTAATTGGGCCCAATAGTCCGGTGCATGTTGACCTCAGG-5

Would the primer pairs 3-AATGC-5 and 5-GCATG3 amplify the same fragment described in Problem
2.25? Explain your answer.
2.27 Suppose that a fragment of human DNA of length
3 kb is to be amplified by PCR. The total genome size
is 3  106 kb, which equals 3  109 base pairs.
(a) Prior to amplification, what fraction of the total
DNA does the target sequence constitute?
(b) What fraction does it constitute after 10 cycles of
PCR?
(c) After 20 cycles of PCR?
(d) After 30 cycles of PCR?
2.28 Some polymorphisms can be identified using oligonucleotides with randomly chosen sequences as
primers. These are known as RAPD polymorphisms,
where RAPD stands for randomly amplified polymorphic
DNA. Typically, the primer oligionucleotides are sufficiently short that they will hybridize at multiple
sites in the genome, and thus serve to amplify multiple fragments. An amplified fragment is regarded as
polymorphic if it can be amplified in some individuals but not others. The accompanying gel diagram
shows a typical pattern observed with randomly
amplified DNA from four individuals. In this case,
which bands are the RAPD polymorphisms?
2.26

12
10
8
Band
number
6

Locus 2

Locus 3

2.30

A woman is uncertain which of two men is the father

of her child. DNA typing is carried out on blood from
the child (C), the mother (M), and on the two males
(A and B), using probes for a highly polymorphic
DNA marker on two different chromosomes
(locus 1 and locus 2). The result is shown in the
accompanying diagram. Does either or both of the
tested loci rule out any of the males as being the possible father? Explain your reasoning.
A

4
2

2.29

A cigarette butt found at the scene of a robbery is

found to have a sufficient number of epithelial cells
stuck to the paper that the DNA can be extracted and
analyzed by DNA typing. Shown here are the results
of typing for three probes (locus 1locus 3) of the
evidence (X) and cells from seven suspects (AG).
Which of the suspects can be excluded? Which cannot be excluded? Can you identify the perpetrator?
Explain you reasoning.

Locus 1

Locus 2

Analysis and Applications

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