Pyranosyl-RNA ('p-RNA'): NMR and molecular-dynamics study of the duplex formed by self-pairing of ribopyranosyl-(C-G-A-A-T-T-C-G)

The solution structure of the duplex formed by seif-pairing of the p-RNA octamer beta-D-ribopyranosyl(2'-->4')-(CGAATTCG) was studied by NMR techniques and, independently, by molecular-dynamics calculations. The resonances of all non-exchanging protons, H-bearing C-atoms, P-atoms, and of most NH protons were assigned. Dihedral angle and distance constraints derived from coupling constants and NOESY spectra are consistent with a single dominant conformer and corroborate the main structural features predicted by qualitative conformational analysis. The duplex displays Watson-Crick pairing with antiparallel strand orientation. The dihedral angles beta and epsilon in the phosphodiester linkages differ considerably from the idealized values. Model considerations indicate that these deviations from the idealized model allow better interstrand stacking and lessen unfavorable interactions in the backbone. The average base-pair axis forms an angle of ca. 40 degrees with the backbone. The resulting inter strand pi-pi stacking between either two purines, or a purine and a pyrimidine, but not between two pyrimidines, constitutes a characteristic structural feature of the p-RNA duplex. A 1000-ps molecular-dynamics (MD) calculation with the AMBER force field resulted in an average structure of the same conformation type as derived by NMR. for the backbone torsion angle epsilon, dynamically averaged coupling constants from the MD calculation agree well with the experimental values, but for the angle beta, a systematic difference of ca. 25 degrees remains. The two base pairs at the ends of the duplex are calculated to be highly labile, which is consistent with the high exchange rate of the corresponding imino protons found by NMR.