The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC)center dot d(GCTTCTCTTC) shows significant differences to that found in solution

The crystal structure of the RNA/DNA hybrid r(GAAGA-GAAGC).d(GCTTCTCTTC) ha s been solved and refined at 2.5 Angstrom resolution. The refinement proced ure converged at R = 0.181 for all reflections in the range 20.0-2.5 Angstr om, In the crystal, the RNA/DNA hybrid duplex has an A' conformation with a ll but one of the nucleotide sugar moieties adopting a C3'-endo (N) conform ation. Both strands in the double helix adopt a global conformation close t o the A-form and the width of the minor groove is typical of that found in the crystal structures of other A-form duplexes. However, differences are o bserved between the RNA and DNA strands that make up the hybrid at the loca l level. In the central portion of the duplex, the RNA strand has backbone alpha, beta and gamma torsion angles that alternate between the normal gauc he(-)/trans/ gauche(+) conformation and an unusual trans/trans/trans confor mation. Coupled with this so-called 'alpha/gamma flipping' of the backbone torsion angles, the distance between adjacent phosphorous atoms on the RNA strand systematically varies. Neither of these phenomena are observed on th e DNA strand. The structure of the RNA/DNA hybrid presented here differs si gnificantly from that found in solution for this and other sequences. Possi ble reasons for these differences and their implications for the current mo del of RNase H activity are discussed.