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.
Chuprina
V P
VP
Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region.
Nerdal
W
W
Sletten
E
E
Poltev
V I
VI
Fedoroff OYu
D001483:Base Sequence; D002236:Carbohydrate Conformation; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D003855:Deoxyribose / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011687:Purines / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*
D011687:Purines; D011743:Pyrimidines; D003855:Deoxyribose; D004247:DNA; C030986:pyrimidine; C030985:purine