The DNA strand in DNA.cntdot.RNA hybrid duplexes is neither B-form nor A-form in solution

Abstract

The structure of the DNA.RNA hybrid (GTCACATG).(caugugac), where lowercase 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. (1983) Eur. J. Biochem. 135, 307-314] via one-dimensional NOE methods and circular dichroism studies. Contrary to their results, we find that this duplex does not assume a B-form conformation in solution. Instead, the RNA residues retain their C3'-endo (A-form) conformation, as indicated by the absence of H1'-H2' couplings and by strong H6/H8 to (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 intermediate conformation in the O4'-endo range (P approximately 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 H1'-H2' coupling constants that are of approximately the same magnitude as the H1'-H2" coupling constants. These results suggest that the RNA strand not only retains its N-type structure but also exerts an influence on the conformation of the DNA strand. Our results provide strong 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 conformation in solution. Furthermore, although not the main focus of this 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, 3940-3946).

The Bacterial Histone-like Protein HU Specifically Recognizes Similar Structures in All Nucleic Acids

“…The conformations of B-DNA and A-RNA are known to differ significantly, while DNA-RNA hybrids were shown to assume an intermediate A/B conformation (42). Nevertheless, HU seemed to recognize both the A and B conformations of RNA and DNA duplexes.…”

“…This probably reflects a more advantageous orientation of tandemly bound HU molecules along the A-helix for dimer-dimer interactions. It is also noteworthy that HU exhibited in its binding to DNA-RNA hybrids more resemblance to dsDNA than was seen for dsRNA, even though the DNA-RNA heteroduplex assumed the intermediate A/B conformation (42). Interestingly, the Z␣ domain of dsRNA adenosine deaminase (ADAR1) was demonstrated to bind left-handed Z-RNA specifically, as well as Z-DNA, and to stabilize the Z-conformation (45).…”

Base-Displaced Intercalated Structure of the Food Mutagen 2-Amino-3-methylimidazo[4,5-f]quinoline in the Recognition Sequence of the NarI Restriction Enzyme, a Hotspot for −2 bp Deletions

“…75 The J H1′-H2′ and J H1′-H2″ couplings were measured from the E-COSY experiment, 69 whereas the intensities of J H2″-H3′ and J H3′-H4′ couplings were determined from the DQF-COSY experiment. The data were fit to curves relating the coupling constants to pseudorotation (P), sugar pucker amplitude (ϕ), and the percentage S-type conformation.…”

Crystal structure of RNA-DNA duplex provides insight into conformational changes induced by RNase H binding

“…Unlike hybrid structures determined by NMR or duplexes bound to RNase H, the GAA duplex is primarily C3 0 -endo in both the RNA and DNA strands whereas bound hybrids and those determined by NMR have an RNA strand with a C3 0 -endo and a DNA strand with C2'-endo, or related, sugar conformation. [22][23][24][30][31][32] To examine how the sequence of the GAA duplex affected the overall structure of the hybrid as compared to previously determined hybrid structures composed of polypurine and polypyrimidine tracks (PPT), 2 PPT RNA-DNA hybrid structures (PDB: 1G4Q and 3SSF) were used as comparative models with the GAA structure. As shown in Table 3, the helical parameters calculated for the other RNA-DNA hybrids are generally similar to the GAA structure with the notable difference that the width of the major groove for GAA is smaller by 0.3 A than the RNA-DNA and PPT hybrids.…”