DNA conformations and their sequence preferences

Nucleic Acids Res. 2008 Jun;36(11):3690-706. doi: 10.1093/nar/gkn260. Epub 2008 May 13.

Abstract

The geometry of the phosphodiester backbone was analyzed for 7739 dinucleotides from 447 selected crystal structures of naked and complexed DNA. Ten torsion angles of a near-dinucleotide unit have been studied by combining Fourier averaging and clustering. Besides the known variants of the A-, B- and Z-DNA forms, we have also identified combined A + B backbone-deformed conformers, e.g. with alpha/gamma switches, and a few conformers with a syn orientation of bases occurring e.g. in G-quadruplex structures. A plethora of A- and B-like conformers show a close relationship between the A- and B-form double helices. A comparison of the populations of the conformers occurring in naked and complexed DNA has revealed a significant broadening of the DNA conformational space in the complexes, but the conformers still remain within the limits defined by the A- and B- forms. Possible sequence preferences, important for sequence-dependent recognition, have been assessed for the main A and B conformers by means of statistical goodness-of-fit tests. The structural properties of the backbone in quadruplexes, junctions and histone-core particles are discussed in further detail.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cytosine / chemistry
  • DNA / chemistry*
  • DNA, A-Form / chemistry
  • DNA, Cruciform / chemistry
  • DNA-Binding Proteins / chemistry
  • Deoxyribonucleotides / chemistry
  • G-Quadruplexes
  • Ligands
  • Nucleic Acid Conformation
  • Nucleosomes / chemistry
  • RNA / chemistry

Substances

  • DNA, A-Form
  • DNA, Cruciform
  • DNA-Binding Proteins
  • Deoxyribonucleotides
  • Ligands
  • Nucleosomes
  • RNA
  • Cytosine
  • DNA