THE STRUCTURE OF DNA

Perhaps the most exciting aspect of the structure of DNA deduced by Watson and Crick was, as expressed in their words,
that the "specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic
material." A double helix separated into two single strands can be replicated because each strand serves as a template on
which its complementary strand can be assembled .Although this notion of how DNA is replicated is
absolutely correct, the doublehelical structure of DNA poses a number of challenges to replication, as does the need for
extremely faithful copying of the genetic information.
1. The two strands of the double helix have a tremendous affinity for one another, created by the cooperative effects of
the many hydrogen bonds that hold adjacent base pairs together. Thus, a mechanism is required for separating the strands
in a local region to provide access to the bases that act as templates. Specific proteins melt the double helix at specific
sites to initiate DNA replication, and other enzymes, termed helicases, use the free energy of ATP hydrolysis to move
this melted region along the double helix as replication progresses.
2. The DNA helix must be unwound to separate the two strands. The local unwinding in one region leads to stressful
overwinding in surrounding regions .Enzymes termed topoisomerases introduce supercoils that release the
strain caused by overwinding.
3. DNA replication must be highly accurate. As noted in Chapter 5, the free energies associated with base pairing within
the double helix suggest that approximately 1 in 104 bases incorporated will be incorrect. Yet, DNA replication has an
error rate estimated to be 1 per 1010 nucleotides. As we shall see, additional mechanisms allow proofreading of the
newly formed double helix.
4. DNA replication must be very rapid, given the sizes of the genomes and the rates of cell division. The E. coli genome
contains 4.8 million base pairs and is copied in less than 40 minutes. Thus, 2000 bases are incorporated per second. We
shall examine some of the properties of the macromolecular machines that replicate DNA with such high accuracy and
speed.
5. The enzymes that copy DNA polymerize nucleotides in the 5 3 direction. The two polynucleotide strands of DNA
run in opposite directions, yet both strands appear to grow in the same direction .Further analysis reveals
that one strand is synthesized in a continuous fashion, whereas the opposite strand is synthesized in fragments in a
discontinuous fashion. The synthesis of each fragment must be initiated in an independent manner, and then the
fragments must be linked together. The DNA replication apparatus includes enzymes for these priming and ligation
reactions.
6. The replication machinery alone cannot replicate the ends of linear DNA molecules, so a mechanism is required to
prevent the loss of sequence information with each replication. Specialized structures called telomeres are added by
another enzyme to maintain the information content at chromosome ends.
7. Most components of the DNA replication machinery serve to preserve the integrity of a DNA sequence to the
maximum possible extent, yet a variety of biological processes require DNA formed by the exchange of material
between two parent molecules. These processes range from the development of diverse antibody sequences in the
immune system to the integration of viral genomes into host DNA. Specific enzymes, termed
recombinases, facilitate these rearrangements.
8. After replication, ultraviolet light and a range of chemical species can damage DNA in a variety of ways. All
organisms have enzymes for detecting and repairing harmful DNA modifications. Agents that introduce chemical lesions
into DNA are key factors in the development of cancer, as are defects in the repair systems that correct these lesions.
We begin with a review of the structural properties of the DNA double helix.
III. Synthesizing the Molecules of Life 27. DNA Replication, Recombination, and Repair
III. Synthesizing the Molecules of Life 27. DNA Replication, Recombination, and Repair
DNA Can Assume a Variety of Structural Forms
The double-helical structure of DNA deduced by Watson and Crick immediately suggested how genetic information is
stored and replicated. As was discussed earlier the essential features of their model are:
1. Two polynucleotide chains running in opposite directions coil around a common axis to form a right-handed double
helix.
2. Purine and pyrimidine bases are on the inside of the helix, whereas phosphate and deoxyribose units are on the outside.
3. Adenine (A) is paired with thymine (T), and guanine (G) with cytosine (C). An A-T base pair is held together by two
hydrogen bonds, and that of a G-C base pair by three such bonds.

A-DNA Is a Double Helix with Different Characteristics from Those of the More
Common B-DNA
Watson and Crick based their model (known as the B-DNA helix) on x-ray diffraction patterns of DNA fibers, which
provided information about properties of the double helix that are averaged over its constituent residues. The results of xray
diffraction studies of dehydrated DNA fibers revealed a different form called A-DNA, which appears when the
relative humidity is reduced to less than about 75%. A-DNA, like B-DNA, is a right-handed double helix made up of
antiparallel strands held together by Watson-Crick base-pairing. The A helix is wider and shorter than the B helix, and its
base pairs are tilted rather than perpendicular to the helix axis (Figure 27.4).
Many of the structural differences between B-DNA and A-DNA arise from different puckerings of their ribose units
In A-DNA, C-3 lies out of the plane (a conformation referred to as C-3 -endo) formed by the other four
atoms of the furanose ring; in B-DNA, C-2 lies out of the plane (a conformation called C-2 -endo). The C-3 -endo
puckering in A-DNA leads to a 19-degree tilting of the base pairs away from the normal to the helix. The phosphates and
other groups in the A helix bind fewer H2O molecules than do those in B-DNA. Hence, dehydration favors the A form.
The A helix is not confined to dehydrated DNA. Double-stranded regions of RNA and at least some RNA-DNA hybrids
adopt a double-helical form very similar to that of A-DNA. The position of the 2 -hydroxyl group of ribose prevents
RNA from forming a classic Watson-Crick B helix because of steric hindrance the 2 -oxygen atom would
come too close to three atoms of the adjoining phosphate group and one atom in the next base. In an A-type helix, in
contrast, the 2 -oxygen projects outward, away from other atoms.
The Major and Minor Grooves Are Lined by Sequence-Specific Hydrogen-
Bonding Groups
Double-helical nucleic acid molecules contain two grooves, called the major groove and the minor groove. These
grooves arise because the glycosidic bonds of a base pair are not diametrically opposite each other The
minor groove contains the pyrimidine O-2 and the purine N-3 of the base pair, and the major groove is on the opposite
side of the pair. The methyl group of thymine also lies in the major groove. In B-DNA, the major groove is wider (12
versus 6 Å) and deeper (8.5 versus 7.5 Å) than the minor groove .Each groove is lined by potential hydrogen-bond donor and acceptor atoms that enable specific interactions with proteins
. In the minor groove, N-3 of adenine or guanine and O-2 of thymine or cytosine can serve as hydrogen
acceptors, and the amino group attached to C-2 of guanine can be a hydrogen donor. In the major groove, N-7 of guanine
or adenine is a potential acceptor, as are O-4 of thymine and O-6 of guanine. The amino groups attached to C-6 of
adenine and C-4 of cytosine can serve as hydrogen donors. Note that the major groove displays more features that
distinguish one base pair from another than does the minor groove. The larger size of the major groove in B-DNA makes
it more accessible for interactions with proteins that recognize specific DNA sequences.
The Results of Studies of Single Crystals of DNA Revealed Local Variations in
DNA Structure
X-ray analyses of single crystals of DNA oligomers had to await the development of techniques for synthesizing large
amounts of DNA fragments with defined base sequences. X-ray analyses of single crystals of DNA at atomic resolution
revealed that DNA exhibits much more structural variability and diversity than formerly envisaged.
The x-ray analysis of a crystallized DNA dodecamer by Richard Dickerson and his coworkers revealed that its overall
structure is very much like a B-form Watson-Crick double helix. However, the dodecamer differs from the Watson-Crick
model in not being uniform; there are rather large local deviations from the average structure. The Watson-Crick model
has 10 residues per complete turn, and so a residue is related to the next along a chain by a rotation of 36 degrees. In
Dickerson's dodecamer, the rotation angles range from 28 degrees (less tightly wound) to 42 degrees (more tightly
wound). Furthermore, the two bases of many base pairs are not perfectly coplanar .Rather, they are
arranged like the blades of a propeller. This deviation from the idealized structure, called propeller twisting, enhances
the stacking of bases along a strand. These and other local variations of the double helix depend on base sequence. A
protein searching for a specific target sequence in DNA may sense its presence through its effect on the precise shape of
the double helix.
Z-DNA Is a Left-Handed Double Helix in Which Backbone Phosphates Zigzag
Alexander Rich and his associates discovered a third type of DNA helix when they solved the structure of dCGCGCG.
They found that this hexanucleotide forms a duplex of antiparallel strands held together by Watson-Crick base-pairing,
as expected. What was surprising, however, was that this double helix was left-handed, in contrast with the right-handed
screw sense of the A and B helices. Furthermore, the phosphates in the backbone zigzagged; hence, they called this new
form Z-DNA .The Z-DNA form is adopted by short oligonucleotides that have sequences of alternating pyrimidines and purines. High
salt concentrations are required to minimize electrostatic repulsion between the backbone phosphates, which are closer to
each other than in A- and B-DNA. Under physiological conditions, most DNA is in the B form. Although the biological
role of Z-DNA is still under investigation, its existence graphically shows that DNA is a flexible, dynamic molecule.