The I260Q variant of DNA polymerase beta extends mispaired primer termini due to its increased affinity for deoxynucleotide triphosphate substrates

Biochemistry. 2008 Nov 18;47(46):12118-25. doi: 10.1021/bi8011548. Epub 2008 Oct 21.


DNA polymerase beta plays a key role in base excision repair. We have previously shown that the hydrophobic hinge region of polymerase beta, which is distant from its active site, plays a critical role in the fidelity of DNA synthesis by this enzyme. The I260Q hinge variant of polymerase beta misincorporates nucleotides with a significantly higher catalytic efficiency than the wild-type enzyme. In the study described here, we show that I260Q extends mispaired primer termini. The kinetic basis for extension of mispairs is defective discrimination by I260Q at the level of ground-state binding of the dNTP substrate. Our results suggest that the hydrophobic hinge region influences the geometry of the dNTP binding pocket exclusively. Because the DNA forms part of the binding pocket, our data are also consistent with the interpretation that the mispaired primer terminus affects the geometry of the dNTP binding pocket such that the I260Q variant has a higher affinity for the incoming dNTP than wild-type polymerase beta.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Substitution*
  • Base Pair Mismatch
  • Base Pairing / physiology
  • Catalytic Domain / physiology
  • DNA Polymerase beta / chemistry*
  • DNA Polymerase beta / genetics
  • DNA Polymerase beta / metabolism
  • DNA Primers / chemistry*
  • DNA Primers / genetics
  • DNA Primers / metabolism
  • Deoxyribonucleotides / chemistry*
  • Deoxyribonucleotides / genetics
  • Deoxyribonucleotides / metabolism
  • Humans
  • Hydrophobic and Hydrophilic Interactions
  • Mutation, Missense*
  • Protein Structure, Tertiary / physiology


  • DNA Primers
  • Deoxyribonucleotides
  • DNA Polymerase beta