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DNA




Deoxyribonucleic acid (DNA) is the primary chemical
component of chromosomes and the material of which genes
are made. It is sometimes called the "molecule of heredity," because parents
transmit copied portions of their own DNA to offspring during reproduction
and because in doing so they propagate their traits.

In fact, the units of DNA that reside in the nucleus of eukaryotic cells,
and DNA pieces as people typically think of them, are not single molecules.
Rather, they are pairs of molecules, which entwine like vines to form a
"double helix" (top half of the illustration at the right).

Each vine-like molecule, or strand of DNA, is a chemically linked chain of
nucleotides, which each consist of a deoxyribose sugar, a phosphate, and one
of four varieties of "aromatic" bases. Because DNA strands are composed of
these nucleotide subunits, they are polymers.

The diversity of the bases means that four distinct kinds of nucleotide
exist, which are commonly referred to by the identity of their base. These
are adenine (A), thymine (T), cytosine (C), and guanine (G).

In a DNA double helix, two polynucleotide strands come together through
complementary pairing of the bases, which occurs by hydrogen bonding. Each
base forms hydrogen bonds readily to only one other—A to T and C to
G—so that the identity of the base on one strand dictates what base
must face it on the opposing strand. Thus the entire nucleotide sequence of
each strand is complementary to that of the other, and when separated, each
may act as a template with which to replicate the other from free
nucleotides (middle and lower half of the illustration at the right).

Because pairing causes the nucleotide bases to face the helical axis, the
sugar and phosphate groups of the nucleotides run along the outside, and the
two chains they form are sometimes called the "backbones" of the helix. In
fact, it is chemical bonds between the phosphates and the sugars that link
one nucleotide to the next in the DNA strand.

Mechanical Properties Relevant to Biology

Because hydrogen bonds are weak compared to covalent chemical bonds, the
strands of the double helix can be easily separated by enzymes or even, as
in PCR, by gentle heating. On the other hand, gentle heating works only on
pieces of DNA that are less than about 10,000 base pairs (10 kilobase pairs,
or 10 kbp) long. The intertwining of the DNA strands makes long segments
difficult to separate. Enzymes knowns as helicases unwind the strands to
facilitate the advance of sequence-reading enzymes such as DNA polymerase.
The unwinding requires that helicases chemically cleave the phosphate
backbone of one of the strands so that it can swivel around the other.

When the ends of a piece of double-helical DNA are joined so that it forms a
circle, as in plasmid DNA, the strands are topologically knotted. This means
they cannot be separated by gentle heating or by any process that does not
involve breaking a strand. The task of unknotting topologically linked
strands of DNA falls to enzymes known as topoisomerases. Some of these
enzymes unknot circular DNA by cleaving two strands so that another
double-stranded segment can pass through. Unknotting is required for the
replication of circular DNA as well as for various types of recombination in
linear DNA.

The DNA helix can assume one of three slightly different geometries, of
which the "B" form described by James Watson and Francis Crick is believed
to predominate in cells. It is 2 nanometers wide and extends 3.4 nanometers
per 10 bp of sequence. This is also the approximate length of sequence in
which the helix makes one complete turn about its axis (a parameter that
depends on stacking interactions between the bases).

The narrow breadth of the double helix makes it impossible to detect by
conventional electron microscopy, except by heavy staining. At the same
time, the DNA found in many cells can be macroscopic in
length—approximately 5 centimeters long for strands in a human
chromosome. Consequently, cells must compact or "package" DNA to carry it
within them. This is one of the functions of the chromosomes, which contain
spool-like proteins known as histones, around which DNA winds.

The B form of the DNA helix twists 360¡ per 10.6 bp in the absence of
strain. But many molecular biological processes can induce strain. A DNA
segment with excess or insufficient helical twisting is referred to,
respectively, as positively or negatively "supercoiled". DNA in vivo is
typically negatively supercoiled, which facilitates the unwinding of the
double-helix required for RNA transcription.

The two other known double-helical forms of DNA, called A and Z, differ
modestly in their geometry and dimensions. The A form appears likely to
occur only in dehydrated samples of DNA, such those used in crystallography
experiments, and possibly in hybrid pairings of DNA and RNA strands.
Segments of DNA that cells have methylated for regulatory purposes may adopt
the Z geometry, in which the strands turn about the helical axis like a
mirror image of the B form.

Non-helical DNA

DNA also appears in a non-helical, single-stranded form in some viruses.
Because many of the DNA repair mechanisms of cells rely on base-pairing to
work, viruses that carry single-stranded DNA genomes mutate more frequently
than they would otherwise. As a result, such species may adapt more rapidly
to avoid extinction. The result would not be so favorable in more
complicated and more slowly replicating organisms, however, which may
explain why only viruses carry single-stranded DNA. These viruses presumably
also benefit from the lower cost of replicating one strand versus two.

The Role of the Sequence

Within a gene, the identity of the nucleotides and the exact sequence in
which they appear along a DNA strand decide the amino acid sequence of a
protein. Thus, gene sequences are "translated" into (or "encode") amino acid
sequences of proteins. The rules cells use for translation are described by
the genetic code.

In many species of organisms, only a small fraction of the total sequence of
the genome appears to encode protein. The function of the rest is a matter
of speculation. It is known that certain nucleotide sequences specify
affinity for DNA binding proteins, which play a wide variety of vital roles,
such as the control of replication and transcription. These sequences are
frequently called regulatory sequences, and researchers assume that so far
they have identified only a tiny fraction of the total that exist. "Junk
DNA" represents sequences that do not yet appear to contain genes or to have
a function.

Sequence also determines a DNA segment's susceptibility to cleavage by
restriction enzymes, the quintessential tools of genetic engineering. The
position of cleavage sites throughout an individual's genome determines one
kind of an individual's "DNA fingerprint".

DNA Sequence Reading

The asymmetric shape and linkage of nucleotides give DNA strands an
orientation or directionality. Because of this discernable directionality,
close inspection of a double helix reveals that, although the nucleotides of
one strand are "ascending," the others are "descending." This arrangement of
the strands is called "antiparallel".

For reasons of chemical nomenclature, people who work with DNA refer to the
asymmetric termini of each strand as the 5' and 3' ends (pronounced "five
prime" and "three prime"). DNA workers and enzymes alike always read
nucleotide sequences in the "five-prime-to-three-prime" direction.

As a result of their antiparallel arrangement, even if sequences on opposing
strands of DNA were not merely complimentary (as they always are), but
instead were identical, cells could properly translate a gene into a protein
from only one of the two strands: cells can read the sequence of the other
strand only in the reverse of the proper order. However of course, the
sequences of paired strands do not merely run in opposite directions, their
bases at every position are the complement of one another. A translated or
translatable sequence is called a "sense" sequence, and its compliment is
the "antisense" sequence. Somewhat confusingly, it follows then that the
antisense strand is the template for transcription. The resulting transcript
is an RNA replica of the sense strand and is itself a sense sequence.

The fact that the 3' end of one DNA strand flanks the 5' end of the other
makes the arrangement a "crab canon".

The Discovery of DNA and the Double Helix

Working in the 19th century, biochemists initially isolated DNA and RNA
together from cell nuclei. They were relatively quick to appreciate the
polymeric nature of their "nucleic acid" isolates, but realized only later
that nucleotides were of two types—one containing ribose and the other
deoxyribose. It was this subsequent discovery that led to the identification
and naming of DNA as a substance distinct from RNA. Not until 1943 did
Oswald Theodore Avery provide the first compelling evidence that DNA could
carry genetic information.

How this could be true was unimaginable at the time. Because chemical
dissection of DNA samples always yielded the same four nucleotides, the
chemical composition of DNA appeared simple, perhaps even uniform.
Organisms, on the other hand, are fantastically complex individually and
widely diverse collectively. Geneticists did not speak of genes as conveyors
of "information" in such words, but if they had, they would not have
hesitated to quantify the amount of information that genes need to convey as
vast. The idea that information might reside in a chemical in the same way
that it exists in text—as a finite alphabet of letters arranged in a
sequence of unlimited length—had not yet been conceived. It would
emerge upon the discovery of DNA's structure, but few researchers imagined
that DNA's structure had much to say about genetics.

In the 1950s, only a few groups made it their goal to determine the
structure of DNA. These included an American group led by Linus Pauling, and
two in England. At Cambridge University, Crick and Watson were building
physical models using metal rods and balls, in which they incorporated the
known chemical structures of the nucleotides, as well as the known position
of the linkages joining one nucleotide to the next along the polymer. At
King's College, London, Maurice Wilkins and Rosalind Franklin were examining
x-ray diffraction patterns of DNA fibers.

A key inspiration in the work of all of these teams was the discovery in
1948 by Pauling that many proteins included helical (see alpha helix)
shapes. Pauling had deduced this structure from x-ray patterns. Even in the
intitial crude diffraction data from DNA, it was evident that the structure
involved helices. But this insight was only a beginning. There remained the
questions of how many strands came together, whether this number was the
same for every helix, whether the bases pointed toward the helical axis or
away, and ultimately what were the explicit angles and coordinates of all
the bonds and atoms. Such questions motivated the modeling efforts of Watson
and Crick.

In their modeling, Watson and Crick restricted themselves to what they saw
as chemically and biologically reasonable. Still, the breadth of
possibilities was very wide. A breakthrough occurred in 1952, when Erwin
Chargaff visited Cambridge and inspired Crick with a description of
experiments Chargaff had published in 1947. Chargaff had observed that the
proportions of the four nucleotides vary between one DNA sample and the
next, but that for particular pairs of nucleotides—adenine and
thymine, guanine and cytosine—the two nucleotides are always present
in equal proportions.

Watson and Crick had begun to contemplate double helical arrangements, and
they saw that by reversing the directionality of one strand with respect to
the other, they could provide an explanation for Chargaff's puzzling
finding. This explanation was the complementary pairing of the bases, which
also had the effect of ensuring that the distance between the phosphate
chains did not vary along a sequence. Watson and Crick were able to discern
that this distance was constant and to measure its exact value of 2
nanometers from an X-ray pattern obtained by Franklin. The same pattern also
gave them the 3.4 nanometer-per-10 bp "pitch" of the helix. The pair quickly
converged upon a model, which they announced before Franklin herself
published any of her work.

The great assistance Watson and Crick derived from Franklin's data has
become a subject of controversy, and it has angered people who believe
Franklin has not received the credit due to her. The most controversial
aspect is that Franklin's critical X-ray pattern was shown to Watson and
Crick without Franklin's knowledge or permission. Wilkins showed it to them
at his lab while Franklin was away.

Watson and Crick's model attracted great interest immediately upon its
presentation. Arriving at their conclusion on February 21 1953, Watson and
Crick made their first announcement on February 28. Their paper 'A Structure
for Deoxyribose Nucleic Acid' was published on April 25. In an influential
presentation in 1957, Crick laid out the "Central Dogma", which foretold the
relationship between DNA, RNA, and proteins, and articulated the "sequence
hypothesis." A critical confirmation of the replication mechanism that was
implied by the double-helical structure followed in 1958 in the form of the
Meselson-Stahl experiment. Work by Crick and coworkers deciphered the
genetic code not long afterward. These findings represent the birth of
molecular biology.

Watson, Crick, and Wilkins were awarded a Nobel Prize in 1962, by which time
Franklin had died.

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