Section 42
Chapter 41,203

Refinement of the solution structure of the RNA-DNA hybrid 5'-[r (GCA) d (TGC) ]2. Combined use of nuclear magnetic resonance and restrained molecular dynamics

Happ, C.S.; Happ, E.; Clore, G.M.; Gronenborn, A.M.

Febs Letters 236(1): 62-70


ISSN/ISBN: 0014-5793
PMID: 2456957
DOI: 10.1016/0014-5793(88)80286-2
Accession: 041202272

The solution conformation of the self-complementary RNA-DNA hybrid hexamer 5'-[r(GCA)d(TGC)]2 is investigated by NMR spectroscopy and restrained molecular dynamics. The 1H-NMR spectrum is assigned in a sequential manner using two-dimensional homonuclear Hartmann-Hahn and nuclear Overhauser enhancement spectroscopy. From the latter a set of 178 approximate interproton distance restraints are determined and used as the basis of a structure refinement by restrained molecular dynamics. Eight independent calculations are carried out, four from a classical A-type geometry and four from a classical B-type one. Convergence is achieved to very similar A-type structures with an average atomic root mean square difference between them of 1.0 +/- 0.2 A. The converged structures exhibit variations in helical parameters similar to those found previously for the analogue RNA hexamer 5'-r(GCAUGC)2 [(1988) Biochemistry 27, 1735-1743].

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