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

FEBS Lett. 1988 Aug 15;236(1):62-70. doi: 10.1016/0014-5793(88)80286-2.


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].

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • DNA*
  • Magnetic Resonance Spectroscopy
  • Nucleic Acid Conformation
  • Nucleic Acid Hybridization*
  • Protons
  • RNA*
  • Software
  • Solutions


  • Protons
  • Solutions
  • RNA
  • DNA