High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A

Nucleic Acids Res. 2011 Aug;39(14):6238-48. doi: 10.1093/nar/gkr202. Epub 2011 Apr 1.

Abstract

The crystal structure of a Z-DNA hexamer duplex d(CGCGCG)(2) determined at ultra high resolution of 0.55 Å and refined without restraints, displays a high degree of regularity and rigidity in its stereochemistry, in contrast to the more flexible B-DNA duplexes. The estimations of standard uncertainties of all individually refined parameters, obtained by full-matrix least-squares optimization, are comparable with values that are typical for small-molecule crystallography. The Z-DNA model generated with ultra high-resolution diffraction data can be used to revise the stereochemical restraints applied in lower resolution refinements. Detailed comparisons of the stereochemical library values with the present accurate Z-DNA parameters, shows in general a good agreement, but also reveals significant discrepancies in the description of guanine-sugar valence angles and in the geometry of the phosphate groups.

Publication types

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

MeSH terms

  • Base Pairing
  • Crystallography, X-Ray
  • DNA, Z-Form / chemistry*
  • Models, Molecular
  • Stereoisomerism
  • Water / chemistry

Substances

  • DNA, Z-Form
  • Water