Base Dependence of B-DNA Sugar Conformation in Solution and in the Solid State

Abstract

Analysis of 1H-NOESY solution data for eight short DNA duplexes has revealed pronounced differences between the sugar conformations of purine and pyrimidine nucleotides. It was found that the H1′-H4′ interproton distance is less than ca. 3.0 A. in pyrimidine sugars, while in purine sugars it is more than ca. 3.OA. This difference has been analyzed by comparison with the sugar conformations of highly resolved B-DNA crystal structures and model sugar conformations. The conclusion can be drawn that the deoxyribose conformation is of the general C2′-endo type but pyrimidine sugars are characterized by smaller phase angles of pseudorotation P (90°<P<150°), while purine sugars have larger P values that are greater than ca. 140° (140°<P<180°). There is no such clear base dependence of sugar conformation in highly resolved B-DNA crystal structures; however the similar trend can be seen as in the solution studies. Based on B-type DNA crystal structures, I-coupling constants have been calculated, and the applicability of experimental coupling measurements to the determination of sugar conformation is discussed.