Nucleic Acids Research, Vol 27, Issue 2 555-561, Copyright © 1999 by Oxford University Press
GL Conn, T Brown and GA Leonard
The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC)
has been solved and refined at 2.5 A resolution. The refinement procedure
converged at R = 0.181 for all reflections in the range 20.0-2.5 A. In the
crystal, the RNA/DNA hybrid duplex has an A' conformation with all but one
of the nucleotide sugar moieties adopting a C3'- endo (N) conformation.
Both strands in the double helix adopt a global conformation close to 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
observed between the RNA and DNA strands that make up the hybrid at the
local level. In the central portion of the duplex, the RNA strand has
backbone alpha, beta and gamma torsion angles that alternate between the
normal gauche -/ trans / gauche + conformation and an unusual trans / trans
/ trans conformation. 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 the DNA strand. The structure of the RNA/DNA hybrid
presented here differs significantly from that found in solution for this
and other sequences. Possible reasons for these differences and their
implications for the current model of RNase H activity are discussed.
ARTICLES
The crystal structure of the RNA/DNA hybrid r(GAAGAGAAGC). d(GCTTCTCTTC) shows significant differences to that found in solution
Department of Chemistry, University of Southampton, Southampton SO17 1BJ, UK and Joint ESRF/EMBLStructural Biology Group, European Synchrotron Radiation Facility, BP 200, F-38034 Grenoble Cedex, France.
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