Base pair bonding patterns

Figure 7.7 Color codes for the recognition patterns at the edges of the base pairs in the major (a) and minor (b) grooves of B-DNA. Hydrogen-bond acceptors are red hydrogen-bond donors are blue. The methyl group of thymine is yellow, while the corresponding H atom of cytosine is white.

As with proteins, the nucleic acid polymers can denature, and they have secondary structure. In DNA, two nucleic acid polymer chains are twisted together with their bases facing inward to form a double helix. In doing so, the bases shield their hydrophobic components from the solvent, and they form hydrogen bonds in one of only two specific patterns, called base pairs. Adenine hydrogen bonds only with thymine (or uracil in RNA), and guanine pairs only with cytosine. Essentially every base is part of a base pair in DNA, but only some of the bases in RNA are paired. The double-helix structure... 

The various base pairs, e.g. A T vs G C, can be individually distinguished based on their pattern of H-bond donors and H-bond acceptors, as viewed from the major groove (Fig. 1.11). 

Fig. 1.11. H -bond donors (D) and H-bond acceptors (A) in A T and G C base pairs. Schematic display of the differing pattern of H-bond acceptors and donors in the Watson-Crick base pairs. The groups above the base pairs (above the line) are accessible in the major groove, and those below the line are accessible from the minor groove.

While searching for the meaning of these equalities, James Watson noted that hydrogen-bonded base pairs with the same overall dimensions could be formed between A and T and between G and C (fig. 25.4). The A-T base-paired structure has two hydrogen bonds, whereas the G-C base pair has three. The hydrogen-bonded pairs are formed between bases of opposing strands and can only arise if the directional senses of the two interacting chains are opposite or antiparallel (fig. 25.5). With this notion in mind Francis Crick took a closer look at the x-ray diffraction pattern produced by DNA and was able to interpret the diffraction pattern in terms of a helix (see Methods of Biochemical... 

---