THE DNA STRAND IN DNA.RNA HYBRID DUPLEXES IS NEITHER B-FORM NOR A-FORM IN SOLUTION

The structure of the DNA.RNA hybrid (GTCACATG).(caugugac), where lower case letters designate RNA residues, has been determined on the basis of J-coupling analysis and 2D-NOE studies. The central hexamer in this sequence has been previously studied [Reid, D. G., Salisbury, S. A., Brown, T., Williams, D. H., Vasseur, J.-J., Rayner, B., & Imabach, J.- L. (I 983) Eur. J. Biochem. 135, 307-314] via one-dimensional NOE meth ods and circular dichroism studies. Contrary to their results, we find that this duplex does not assume a B-form conformation in solution. I nstead, the RNA residues retain their C3'-endo (A-form) conformation, as indicated by the absence of H1'-H2' couplings and by strong H6/H8 t o (n - 1) H2' NOEs. The sugars of the DNA residues, on the other hand, do not assume an A-form (or a B-form) conformation but an intermediat e conformation in the O4'-endo range(P almost-equal-to 72-110-degrees) , as indicated by the presence of strong H1'-H4' NOEs, medium-strength H2''-H3' COSY cross peaks, strong H3'-H4' DQF-COSY cross peaks, and H 1'-H2' coupling constants that are of approximately the same magnitude as the H1'-H2'' coupling constants. These results suggest that the RN A strand not only retains its N-type structure but also exerts an infl uence on the conformation of the DNA strand. Our results provide stron g evidence that DNA.RNA hybrid duplexes do not assume an all-C2'-endo B-type conformation; neither do they assume an all-C3'-endo A-type con formation in solution. Furthermore, although not the main focus of thi s study, a comparison of the longitudinal relaxation times of the DNA and RNA residues indicates the need for extended relaxation delays in two-dimensional NMR spectra of hybrid duplexes, as has been previously observed for DNA.RNA chimeric duplexes (Wang, A. C., Kim, S.-G., Chou , S.-H., Orban, J., Flynn, P., & Reid, B. R. (1992) Biochemistry 31, 3 940-3946).