Sugar conformation of a stereospecific 2′-R or 2′-S deuterium-labeled DNA decamer studied with proton-proton J coupling constants

Abstract

The sugar conformation of a DNA decamer was studied with proton-proton ³J coupling constants. Two samples, one comprising stereospecifically labeled 2′-R-²H for all residues and the other 2′-S-²H, were prepared by the method of Kawashima et al. [J. Org. Chem. (1995) 60, 6980–6986; Nucleosides Nucleotides (1995) 14, 333–336], the deuterium labeling being highly stereospecific ≥ 99% for all 2′′-²H, ≥ 98% for 2′-²H of A, C, and T, and ≥ 93% for 2′-²H of G). The ³J values of all H1′-H2′ and H1′-H2′′ pairs, and several H2′-H3′ and H2′′-H3′ pairs were determined by line fitting of 1D spectra with 0.1–0.2 Hz precision. The observed J coupling constants were explained by the rigid sugar conformation model, and the sugar conformations were found to be between C3′-exo and C2′-endo with Φ_m values of 26° to 44°, except for the second and 3′ terminal residues C2 and C10. For the C2 and C10 residues, the lower fraction of S-type conformation was estimated from J_H1′H2′ and J_{H1′H2′′} values. For C10, the N–S two-site jump model or Gaussian distribution of the torsion angle model could explain the observed J values, and 68% S-type conformation or C1′-exo conformation with 27° distribution was obtained, respectively. The differences between these two motional models are discussed based on a simple simulation of J-coupling constants.