Pairing geometry of the hydrophobic thymine analogue 2,4-difluorotoluene in duplex DNA as analyzed by X-ray crystallography

J Am Chem Soc. 2009 Sep 9;131(35):12548-9. doi: 10.1021/ja905739j.

Abstract

Certain DNA polymerases (pols) were found to efficiently insert A opposite the hydrophobic T isostere 2,4-difluorotoluene (F) and vice versa, resulting in the widely held belief that some pols rely on shape rather than H-bonding for accurate replication. Using X-ray crystallography we have analyzed the geometry of F:A pairs in duplex DNA and observed a distance between fluorine and the exocyclic amino group of A that is consistent with a H-bond, thus challenging the assumption that the F analogue is unable to engage in H-bonding as well as the steric hypothesis of DNA replication. Therefore, shape and H-bonding are inherently related, and steric constraints at a pol active site, or conferred by stacking or the DNA backbone conformation, may enable H-bonding by F.

Publication types

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

MeSH terms

  • Bacillus / enzymology
  • Base Pairing*
  • Base Sequence
  • Crystallography, X-Ray
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism
  • Hydrophobic and Hydrophilic Interactions*
  • Models, Molecular
  • Ribonuclease H / metabolism
  • Thymine / analogs & derivatives*
  • Toluene / analogs & derivatives*
  • Toluene / chemistry

Substances

  • Toluene
  • difluorotoluene
  • DNA
  • Ribonuclease H
  • Thymine