Abstract

The unique Watson–Crick arrangement of hydrogen-bonded bases in DNA accommodates two different, complementary purine–pyrimidine pairs, A·T = T·A and G·C = C·G, in a common spatial setting. Nature takes advantage of these isomorphous structures, which store genetic information in terms of the proton donor and acceptor atoms that hold the bases in place. As outlined here, the Watson–Crick base pairs carry other chemical signals that are used to recognize and to process specific sequences of bases. The relative stabilities of G·C versus A·T pairs reflect their different electronic structures. The distributions of electronic charge on the exposed major-groove and minor-groove edges of the base pairs present unique motifs for direct sequence recognition, and the deformations of the paired bases from ideal, planar configurations provide subtle, indirect recognition elements. The biologic significance of the latter signals is not fully understood but is becoming clearer as more and more high-resolution structures of DNA and RNA are determined.