Kinetics of deoxy-CTP incorporation opposite a dG-C8-N-2-aminofluorene adduct by a high-fidelity DNA polymerase

J Mol Biol. 2009 Mar 6;386(4):951-61. doi: 10.1016/j.jmb.2008.12.067. Epub 2009 Jan 3.


The model carcinogen N-2-acetylaminofluorene covalently binds to the C8 position of guanine to form two adducts, the N-(2'-deoxyguanosine-8-yl)-aminofluorene (G-AF) and the N-2-(2'-deoxyguanosine-8-yl)-acetylaminofluorene (G-AAF). Although they are chemically closely related, their biological effects are strongly different and they are processed by different damage tolerance pathways. G-AF is bypassed by replicative and high-fidelity polymerases, while specialized polymerases ensure synthesis past of G-AAF. We used the DNA polymerase I fragment of a Bacillus stearothermophilus strain as a model for a high-fidelity polymerase to study the kinetics of incorporation of deoxy-CTP (dCTP) opposite a single G-AF. Pre-steady-state kinetic experiments revealed a drastic reduction in dCTP incorporation performed by the G-AF-modified ternary complex. Two populations of these ternary complexes were identified: (i) a minor productive fraction (20%) that readily incorporates dCTP opposite the G-AF adduct with a rate similar to that measured for the adduct-free ternary complexes and (ii) a major fraction of unproductive complexes (80%) that slowly evolve into productive ones. In the light of structural data, we suggest that this slow rate reflects the translocation of the modified base within the active site, from the pre-insertion site into the insertion site. By making this translocation rate limiting, the G-AF lesion reveals a novel kinetic step occurring after dNTP binding and before chemistry.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • Cytidine Triphosphate / metabolism*
  • DNA Adducts
  • DNA-Directed DNA Polymerase / metabolism*
  • Deoxyguanosine / metabolism*
  • Elements
  • Fluorenes / metabolism*
  • Geobacillus stearothermophilus / enzymology
  • Guanine
  • Kinetics
  • Phosphorothioate Oligonucleotides / metabolism
  • Substrate Specificity
  • Titrimetry


  • DNA Adducts
  • Elements
  • Fluorenes
  • Phosphorothioate Oligonucleotides
  • 2-aminofluorene
  • Guanine
  • Cytidine Triphosphate
  • DNA-Directed DNA Polymerase
  • Deoxyguanosine