NMR Studies of DNA Structures Containing Sheared Purine•Purine and Purine•Pyrimidine Base Pairs

Abstract

Summary Sheared purine•purine or purine•pyrimidine base pairs are important motifs in nucleic acid structures. They can exist either as tandem base pairs or as a single base pair closing hairpin mini-loops. Presence of such stable motifs greatly increases the structural repertoire of nucleic acid molecules and may play important roles in the contemporary nucleic acid studies. Several RNA crystal structures containing adjacent cross-strand base stacking have been solved. In this review, I will discuss the NMR studies and structural features for DNA molecules containing sheared G•A, A•A, or A•C base pairs. Special attention will be focused on exchangeable proton data, which have turned out to be crucial to the determination of unusual nucleic acid structures. The special features of the partial HIV-1 RT 21-mer act as a good example for correlating the 31P chemical shifts to the ζ and α torsional angles of the backbone phosphate diesters.