Raman spectral studies of nucleic acids. 36. Structure in solution of the RNA.cntdot.DNA hybrid (rA)8.cntdot.(dT)8 determined by NMR and Raman spectroscopy

Abstract

The solution structure of the hybrid RNA{center dot}DNA octamer (rA){sub 8}{center dot}(dT){sub 8} has been determined by nuclear magnetic resonance and laser Raman spectroscopy. The nuclear Overhauser effects resulting from irradiation of thymidine imino protons indicate a duplex structure with conventional Watson-Crick base pairs. The combined results from NMR and Raman spectra are consistent with different nucleotide backbone geometries in (rA){sub 8} and (dT){sub 8} strands. Nucleotide residues of the riboadenylate strand exhibit C3{prime} endo sugar pucker and phosphodiester conformation similar to that of aqueous RNA (the so-called A-form geometry), while residues of the thymidylate strand exhibit C2{prime} endo sugar pucker and phosphodiester conformation similar to that of aqueous DNA (B-form geometry). The solution structure of the hybrid octamer is therefore similar to that proposed previously for poly(rA){center dot}poly(dT) on the basis of fiber X-ray diffraction and solution spectroscopic studies.