Q5(a). DNA bases and Watson–Crick pairing

Introduction. DNA contains four heterocyclic bases: two purines (fused pyrimidine + imidazole rings), adenine (A) and guanine (G), and two pyrimidines (single six-membered ring), cytosine (C) and thymine (T). Each base is bonded to C-1' of 2-deoxyribose by a β-N-glycosidic bond: through N-9 in purines and N-1 in pyrimidines (the N–H shown below).

Scheme: Purines A and G (two rings); pyrimidines C and T (one ring). Thymine is 5-methyluracil.

Base pairing (Watson–Crick)

Scheme: Dashed lines: N–H…N and N–H…O hydrogen bonds between the paired bases.

1. A purine always pairs with a pyrimidine, so every base pair has the same width and fits the regular double helix.
2. A–T: two hydrogen bonds, N6–H (A)…O4 (T) and N3–H (T)…N1 (A).
3. G–C: three hydrogen bonds, N1–H (G)…N3 (C), N2–H (G)…O2 (C) and N4–H (C)…O6 (G). G–C pairs are therefore stronger, and GC-rich DNA melts at a higher temperature.
4. The bases must be in their amino and keto (lactam) tautomers; the rare imino or enol tautomers would mispair (a source of point mutations).
5. Pairing is complementary: in double-stranded DNA [A] = [T] and [G] = [C] (Chargaff's rules). The two strands are antiparallel and the flat pairs stack inside the helix, the sugar–phosphate backbones outside.

Conclusion. DNA has the purines adenine and guanine and the pyrimidines cytosine and thymine. Complementary A=T (two H-bonds) and G≡C (three H-bonds) pairing of purine with pyrimidine holds the two antiparallel strands of the double helix together.

Application. Complementary pairing is the basis of replication, transcription and of laboratory methods such as PCR, DNA hybridisation probes and sequencing.