major groove

minor groove

Thus, there are characteristic patterns of hydrogen bonding ami of overall shape that are exposed in the major groove that distinguish an A:T base pair from a G:C base pair, and, for that matter, A:T from T:A, and C:C from C;G. We can think of these features as a code in which A represents a hydrogen bond acceptor, D a hydrogen bond donor, M a methyl group, and H a nonpolar hydrogen. In such a code, ADAM in the major groove signifies an A:T base pair, and A A D H stands for a G:C base pair. Likewise, M A D A stands for a TA base pair and H D A A is characteristic of a C;G base pair, in all cases, this code of chemical groups in the major groove specifies the identity of the base pair. These patterns are important because they allow proteins to unambiguously recognize DNA sequences without having to open and thereby disrupt the double helix. Indeed, as we shall see, a principal decoding mechanism relies upon the ability of amino acid side chains to protrude into the major groove and to recognize and bind to specific DNA sequences.

The minor groove is not as ritih In chemical information and what information is available is less useful for distinguishing between base pairs. The small size of the minor groove is less able to accommodate amino acid side chains. Also, A:T and T:A base pairs and G:C and C:G base pairs look similar to one another in the minor groove. An A:T base pair has a hydrogen bond acceptor (at N3 of adenine), a nonpolar hydrogen (at N2 of adenine) and a hydrogen bond acceptor (the carbonyl on C2 of thymine). Thus, its code is A H A. But this code is the same if read

77»c Structures of DNA and HNA

in the opposite direction, and hence an A:T base pair does not look very different from a T:A base pair from the point of view of the hydrogen-bonding properties of a protein poking its side chains into the minor groove. Likewise, a CkC base pair exhibits a hydrogen bond acceptor (at IN3 of guanine), a hydrogen bond donur (the exocyclic amino group on C2 of guanine), and a hydrogen bond acceptor (the carbonyl on C2 of cytosine], representing the code ADA, Thus, from the point of view of hydrogen bonding, C:G and G:C base pairs do not li>ok very different from each other either. The minor groove does look different when comparing an A:T base pair with a G:C base pair, but G:C and C.:G, or A:T and T: A, cannot be easily distinguished (see Figure 6-10).

The Double Helix Exists in Multiple Conformations

Early X-ray diffraction studies nf DNA, which were carried out using concentrated solutions of DNA that had been drawn out into thin fibers, revealed two kinds of structures, the B and the A forms of DNA (Figure 6-11). The ti form, which is observed at high humidity, most closely corresponds to the average structure of DNA under physiological conditions. It has 10 base pairs per turn, and a wide major groove and a narrow minor groove. The A form, which is observed under conditions of low humidity, has 11 base pairs per turn. Its major groove is narrower and much deeper than that of the B form, and its minor groove is broader and shallower. The vast majority of the DNA in the cell is in the B form, but DNA does adopt the A structure in certain DNA-protein complexes. Also, as we shall see, the A form is similar to tht; structure that RNA adopts when double helical.

The B form of DNA represents an ideal structure that deviates in two respects from the DNA in cells. First, DNA in Solution, as we have seen, is somewhat more twisted on average than the B form, having on b A DNA

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