Refinement of the solution structure of the B DNA hexamer 5'd(C-G-T-A-C-G)2 on the basis of inter-proton distance data

J Mol Biol. 1985 Sep 5;185(1):219-26. doi: 10.1016/0022-2836(85)90195-0.


A restrained least-squares refinement of the solution structure of the self-complementary B DNA hexamer 5'd(C-G-T-A-C-G)2 is presented. The structure is refined on the basis of 190 inter-proton distances determined by pre-steady-state nuclear Overhauser enhancement measurements. Two refinements were carried out starting from two initial B DNA structures differing by an overall root-mean-square (r.m.s.) difference of 0.32 A. In both cases, the final r.m.s. difference between the experimental and calculated inter-proton distances was 0.12 A compared to 0.61 A and 0.58 A for the two initial structures. The difference between the two refined structures is small, with an overall r.m.s. difference of 0.16 A, and represents the error in the refined co-ordinates. The refined structures have a B-type conformation with local structural variations in backbone and glycosidic bond torsion angles, and base-pair propellor twist, base roll, base tilt and local helical twist angles.

MeSH terms

  • Crystallography
  • DNA*
  • Models, Molecular
  • Nucleic Acid Conformation
  • Oligonucleotides*
  • Protons
  • Software


  • Oligonucleotides
  • Protons
  • DNA