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 soln. structure of the duplex formed by self-pairing of the p-RNA octamer b-D-ribopyranosyl-(2'->4')-(CGAATTCG) was studied by NMR techniques and, independently, by mol.-dynamics calcns. 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 consts. and NOESY spectra are consistent with a single dominant conformer and corroborate the main structural features predicted by qual. conformational anal. The duplex displays Watson-Crick pairing with antiparallel strand orientation. The dihedral angles b and e in the phosphodiester linkages differ considerably from the idealized values. Model considerations indicate that these deviations from the idealized model allow better inter strand stacking and lessen unfavorable interactions in the backbone. The av. base-pair axis forms an angle of ca. 40 Deg with the backbone. The resulting inter strand p-p stacking between either 2 purines, or a purine and a pyrimidine, but not between 2 pyrimidines, constitutes a characteristic structural feature of the p-RNA duplex. A 1000-ps mol.-dynamics (MD) calcn. with the AMBER force field resulted in an av. structure of the same conformation type as derived by NMR. For the backbone torsion angle e, dynamically averaged coupling consts. from the MD calcn. agree well with the exptl. values, but for the angle b, a systematic difference of ca. 25 Deg remains. The 2 base pairs at the ends of the duplex are calcd. to be highly labile, which is consistent with the high exchange rate of the corresponding imino protons found by NMR. [on SciFinder (R)]

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Helvetica Chimica Acta, 79, 8, 2316-2345

 Record created 2006-02-27, last modified 2018-01-27

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