Section 23.3.2.3. Base pairing

The key to the biological role of DNA is that one of the two purines can pair with only one of the pyrimidines: A with T, and G with C. Hence, genetic information present in one strand is passed on to the complementary strand. The standard two-base pairs are shown in Fig. 23.3.2.7 along with the conventional numbering of the atoms. Backbone sugar and phosphate atoms are primed while base atoms are unprimed, as, for example, C1′ and N9 at opposite ends of a purine glycosydic bond. The G·C base pair is held together by three hydrogen bonds, whereas an A·T pair has only two. This means that A·T pairs show less resistance to propeller twisting (counter-rotation of the two bases about their common long axis), and this will have an effect on minor groove width, as seen later. The patterns of hydrogen-bond acceptors (A) and donors (D) on the major and minor groove edges of base pairs are important elements in recognition of base sequence by drugs and control proteins.

Figure 23.3.2.7| top | pdf | A·T and G·C base pairs with minor groove edge below and major groove edge above. A is a hydrogen-bond acceptor, D is as hydrogen-bond donor.

Other related but nonstandard base pairs are compared in Fig. 23.3.2.8. Inosine (I) is useful in studying properties of DNA in that, when paired with cytosine (C), it creates a G·C-family base pair having overall similarity to A·T. Similarly, diaminopurine (DAP) [also known as 2-aminoadenine (2aA)], when paired with thymine (T), creates a G·C-like pair from A·T-family bases. Hence, in a given experimental situation, one can unscramble the relative significance of number of hydrogen bonds versus identity and location of exocyclic groups.

Figure 23.3.2.8| top | pdf | Alternative purines and pyrimidines, and possible base pairings. Purines: P = purine; AP = 2-aminopurine; A = adenine or 6-aminopurine; DAP = 2,6-diaminopurine (also known as 2aA = 2-aminoadenine); G = guanine; I = inosine. Pyrimidines: T = thymine (uracil if methyl group is absent); C = cytosine. DAP–T is a nonstandard AT-family analogue of G–C, and I–C is a nonstandard GC-family analogue of A–T.

The conventional Watson–Crick base pairing of Fig. 23.3.2.7 uses the hexamer `end' of the purine base. A different type of base pairing was proposed many years ago by Hoogsteen (1963), in which the upper edge of the purine was used: N7 and N6/O6. Hoogsteen base pairing is shown between the left-hand two bases in each part of Fig. 23.3.2.9. Note that in Hoogsteen base pairing of A and T, each ring provides both a hydrogen-bond donor and an acceptor. Guanine cannot do this, since both its N7 and O6 positions are acceptors. As a consequence, in a G·C pair, C must supply both of the hydrogen-bond donors. It can only form a Hoogsteen base pair with G when the cytosine ring is protonated. This would lead one to expect triplex formation only at low pH. However, the stability of a triplex can, to a certain extent, alter the pK_a of the N—H proton itself. (Recall the shift in pK_a of buried Asp and His groups in the active sites of enzymes.) Hence, with a single-chain DNA, G-A-G-A-G-A-A-C-C-C-C-T-T-C-T-C-T-C-T-T-T-C-T-C-T-C-T-T, that folds back upon itself twice to build a triplex, NMR experiments indicate a significant amount of triplex remaining even at pH 8.0 (Sklenár & Feigon, 1990; Feigon, 1996).

Figure 23.3.2.9| top | pdf | Watson–Crick pairing of a purine (A or G) with a pyrimidine to its right (T or C), and Hoogsteen pairing of the same purine with a pyrimidine above it. This combination of Watson–Crick and Hoogsteen pairing is found in triple helices or triplexes. Note that Hoogsteen pairing of G and C can only occur at a pH at which C is protonated, because the extra proton is essential for the second hydrogen bond.