Viewing Human DNA Polymerase β Faithfully and Unfaithfully Bypass an Oxidative Lesion by Time-Dependent Crystallography

J Am Chem Soc. 2015 Apr 22;137(15):5225-30. doi: 10.1021/jacs.5b02109. Epub 2015 Apr 9.


One common oxidative DNA lesion, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), is highly mutagenic in vivo due to its anti-conformation forming a Watson-Crick base pair with correct deoxycytidine 5'-triphosphate (dCTP) and its syn-conformation forming a Hoogsteen base pair with incorrect deoxyadenosine 5'-triphosphate (dATP). Here, we utilized time-resolved X-ray crystallography to follow 8-oxoG bypass by human DNA polymerase β (hPolβ). In the 12 solved structures, both Watson-Crick (anti-8-oxoG:anti-dCTP) and Hoogsteen (syn-8-oxoG:anti-dATP) base pairing were clearly visible and were maintained throughout the chemical reaction. Additionally, a third Mg(2+) appeared during the process of phosphodiester bond formation and was located between the reacting α- and β-phosphates of the dNTP, suggesting its role in stabilizing reaction intermediates. After phosphodiester bond formation, hPolβ reopened its conformation, pyrophosphate was released, and the newly incorporated primer 3'-terminal nucleotide stacked, rather than base paired, with 8-oxoG. These structures provide the first real-time pictures, to our knowledge, of how a polymerase correctly and incorrectly bypasses a DNA lesion.

Publication types

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

MeSH terms

  • 8-Hydroxy-2'-Deoxyguanosine / analogs & derivatives
  • Biocatalysis
  • Catalytic Domain
  • Crystallography, X-Ray
  • DNA Damage
  • DNA Polymerase beta / chemistry*
  • DNA Polymerase beta / metabolism*
  • Diphosphates / chemistry
  • Diphosphates / metabolism
  • Guanine / analogs & derivatives
  • Guanine / chemistry
  • Guanine / metabolism
  • Humans
  • Metals / chemistry
  • Metals / metabolism
  • Models, Molecular
  • Oxidation-Reduction
  • Protein Conformation
  • Time Factors


  • Diphosphates
  • Metals
  • Guanine
  • 8-oxo-7,8-dihydrodeoxyguanine
  • 8-Hydroxy-2'-Deoxyguanosine
  • DNA Polymerase beta