Base Pairs Can Combine to Form Triplets and Quadruplets

3 Base Pairs Can Combine to Form Triplets and Quadruplets 

In polymeric nucleic acids, the Watson-Crick base pairs also have the potential to form additional hydrogen bonds. These will generally be saturated by water of hydration molecules. They are, in fact, necessary for specific recognition of a particular nucleic acid base sequence by a particular protein such as, for example, 

The extra hydrogen-bonding sites can, however, also form further base pairs, as observed for poly(A) poly(U). In the Watson-Crick A-U pair, one of the adenine N(6)-H donors and the N(7) acceptor are still free and can form another A-U pair of the Hoogsteen type (Fig. 16.16). This is in fact observed if the Watson-Crick duplex poly(A) poly(U) is exposed to high salt conditions, it disproportionates to form a triplex poly(A)-2poly(U) and a single strand poly(A) [539]  

Base Pairing in the Purine and Pyrimidine Crystal Structures 

Because the glycosyl links and the associated sugar-phosphate backbone are related, in the Watson-Crick duplex, by a pseudodyad perpendicular to the helix axis, the two strands are oriented antiparallel. They are parallel in the Hoogsteen duplex because the glycosyl links are related by rotation about the helix axis. 

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