Base dependence of B-DNA sugar conformation in solution and in the solid state

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. 3.0A. 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 degrees < P < 150 degrees), while purine sugars have larger P values that are greater than ca. 140 degrees (140 degrees < P < 180 degrees). 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, J-coupling constants have been calculated, and the applicability of experimental coupling measurements to the determination of sugar conformation is discussed.