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
Open Access
- 15 August 1988
- journal article
- Published by Wiley in FEBS Letters
- Vol. 236 (1) , 62-70
- https://doi.org/10.1016/0014-5793(88)80286-2
Abstract
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 Å. 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].Keywords
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