Hydrogen and hydration of DNA and RNA oligonucleotides

Abstract

In this paper, hydrogen bonding interaction and hydration in crystal structures of both DNA and RNA oligonucleotides are discussed. Their roles in the formation and stabilization of oligonucleotides have been covered. Details of the Watson–Crick base pairs G·C and A·U in DNA and RNA are illustrated. The geometry of the wobble (mismatched) G·U base pairs and the cis and almost trans conformations of the mismatched U·U base pairs in RNA is described. The difference in hydration of the Watson–Crick base pairs G·C, A·U and the wobble G·U in different sequences of codon–anticodon interaction in double helical molecules are indicative of the effect of hydration. The hydration patterns of the phosphate, the 2′-hydroxyl groups, the water bridges linking the phosphate group, N7 (purine) and N4 of Cs or O4 of Us in the major groove, the water bridges between the 2′-hydroxyl group and N3 (purine) and O2 (pyrimidine) in the minor groove are discussed.