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

The sugar conformation of a DNA decamer was studied with proton-proton (3)J coupling constants. Two samples, one comprising stereospecifically labeled 2'-R-H-2 for all residues and the other 2'-S-H-2, were prepared by the met hod of Kawashima et al. [J. Org. Chem. (1995) 60, 6980-6986; Nucleosides Nu cleotides (1995) 14, 333-336], the deuterium labeling being highly stereosp ecific greater than or equal to 99% for all 2''-H-2, greater than or equal to 98% for 2'-H-2 of A, C, and T, and greater than or equal to 93% for 2'-H -2 of G). The (3)J 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 Phi (m) values of 26 degrees to 44 degrees, 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 estimat ed from J(H1'H2') and J(H1'H2')' values. For C10, the N-S two-site jump mod el or Gaussian distribution of the torsion angle model could explain the ob served J values, and 68% S-type conformation or C1'-exo conformation with 2 7 degrees distribution was obtained, respectively. The differences between these two motional models are discussed based on a simple simulation of J-c oupling constants.