RAMAN SPECTRAL STUDIES OF NUCLEIC-ACIDS .36. STRUCTURE IN SOLUTION OF THE RNA.DNA HYBRID (RA)8.(DT)8 DETERMINED BY NMR AND RAMAN-SPECTROSCOPY

The solution structure of the hybrid RNA·DNA octamer (rA)8·(dT)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)8 and (dT)8 strands. Nucleotide residues of the riboadenylate strand exhibit C3' 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' 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)·poly(dT) on the basis of fiber X-ray diffraction1 and solution spectroscopic studies.2-6 In the model developed here for (rA)8·(dT)8, the distance between the C8-H proton and the phosphoester O5' atom of each adenylate residue is 2.2 Å, which is sufficient for an intranucleotide C8-H…O5' hydrogen bond. The presence of intranucleotide C8-H…O5' hydrogen bonds in (rA)n·(dT)n solution structures would explain the previously reported resistance of adenine C8-H protons of poly(rA)·poly(dT) to deuterium isotope exchange in D2O solution.5. © 1990, American Chemical Society. All rights reserved.