Determination of glycosidic bond conformations of pyrimidine nucleosides and nucleotides using vicinal carbon–proton coupling constants

Abstract

Measurements have been made of ³J(C-6,H-1′) and ³J(C-2,H-1′) magnitudes of pyrimidine nucleosides and nucleotides in solution by natural abundance, ¹³C n.m.r. spectroscopy and the results have been interpreted in terms of the glycosidic bond conformations of the nucleic acid derivatives. Based on X-ray crystal structure results a four-state conformational model for the glycosidic bond is introduced consisting of an equilibrium between two syn and two anti conformations; each syn or anti conformation is symmetrically related to the C-1′–H-1′ bond direction and appropriate syn and anti conformations are symmetrically related by 180°. It is shown that a quantitative estimate of the glycosidic bond conformation may be determined from the sum of observed coupling constants [i.e., ΣJ=J(C-6,H-1′)+J(C-2,H-1′)] and that the equilibrium composition of syn and anti conformers may be determined from the difference in observed coupling constants, i.e., ΔJ=J(C-6,H-1′)–J(C-2,H-1′). Results for uridine and cytidine derivatives are discussed.