DNA variability in five crystal structures of d(CGCAATTGCG)

Acta Crystallogr D Biol Crystallogr. 2004 Apr;60(Pt 4):680-5. doi: 10.1107/S0907444904002896. Epub 2004 Mar 23.

Abstract

The deoxyoligonucleotide d(CGCAATTGCG) has previously been crystallized in four different space groups. The crystals diffract to moderate resolution (2.3-2.9 A). Here, a fifth crystal form that diffracts to higher resolution (1.6 A) is presented which was obtained thanks to the use of Co2+ and cryogenic temperatures. The availability of five different crystal structures allows a thorough analysis of the conformational variability of this DNA sequence. It is concluded that the central hexamer sequence CAATTG has a practically constant conformation under all conditions, whilst the terminal base pairs at both ends vary considerably as a result of differing interactions in the crystals. The new crystal structure presented here is stabilized by guanine-Co2+-guanine interactions and the formation of C1+ -G8.C3 triplexes between neighbouring duplexes. As a result of the higher resolution of the crystal structure, a more regular structure was obtained and a clear definition of the spine of hydration was observed which was not visible in the four previous structures.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • Base Sequence
  • Cobalt / chemistry
  • Crystallization
  • Crystallography, X-Ray
  • DNA / chemistry*
  • Deoxyribonucleotides / chemistry*
  • Guanine / chemistry
  • Models, Molecular
  • Nucleic Acid Conformation

Substances

  • Deoxyribonucleotides
  • Cobalt
  • Guanine
  • DNA