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

Abstract

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 Å. In both cases, the final r.m.s. difference between the experimental and calculated inter-proton distances was 0.12 Å compared to 0.61 Å and 0.58 Å for the two initial structures. The difference between the two refined structures is small, with an overall r.m.s. difference of 0.16 Å, 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.