STRUCTURAL INFLUENCE OF RNA INCORPORATION IN DNA - QUANTITATIVE NUCLEAR-MAGNETIC-RESONANCE REFINEMENT OF D(CG)R(CG)D(CG) AND D(CG)R(C)D(TAGCG)

RNA and DNA adopt different types of conformations, i.e., A-type with C3'-endo sugar pucker for RNA and B-type with C2'-endo sugar pucker fo r DNA, respectively. The structural influence of the incorporation of RNA nucleotides into DNA is less understood. In this paper, we present the three-dimensional structures of two RNA-containing oligonucleotid es, d(CG)r(CG)d(CG) and d(CG)r(C)d(TAGCG), as determined by the NMR re finement procedure, and assess the possible structural perturbation of DNA induced by RNA. With a single RNA insertion into an octamer DNA, its overall conformation remains as the canonical B-DNA, except that t he sugar pucker of the rC3 residue is C3'-endo (pseudorotation angle P = 3.6-degrees). In contrast, the hybrid hexamer is neither the pure B -DNA nor the pure A-DNA conformation. Instead, we propose a model in w hich the DNA parts adopt B conformation, whereas the RNA part adopts A conformation, with the overall conformation closer to A-DNA. To ensur e an exhaustive search of the conformational space, the model was subj ected to 100-ps simulated annealing with slow cooling or 100-ps molecu lar dynamics with subsequent quenching. Models obtained at different t ime points of the trajectories were further subjected to the SPEDREF N OE refinement [Robinson & Wang (1992) Biochemistry 31, 3524] and they appeared to arrive at a convergent model (<0.5 angstrom RMSD for the c entral four base pairs). The consensus hexamer structure contains a si gnificant discontinuity at the (rG4)p(dC5) step with a base pair tilt angle of 6.7-degrees and roll angle of 11.5-degrees. This discontinuit y may be related to the structural ''bend'' that occurs at the junctio n of the RNA and DNA helices.