Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies

Nucleic Acids Res. 2006 Jul 4;34(11):3326-37. doi: 10.1093/nar/gkl425. Print 2006.


Bulky carcinogen-DNA adducts commonly cause replicative polymerases to stall, leading to a switch to bypass polymerases. We have investigated nucleotide incorporation opposite the major adduct of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in the DinB family polymerase, Dpo4, using molecular modeling and molecular dynamics (MD) simulations. PhIP, the most prevalent heterocyclic aromatic amine formed by cooking of proteinaceous food, is mutagenic in mammalian cells and is implicated in mammary and colon tumors. Our results show that the dG-C8-PhIP adduct can be accommodated in the spacious major groove Dpo4 open pocket, with Dpo4 capable of incorporating dCTP, dTTP or dATP opposite the adduct reasonably well. However, the PhIP ring system on the minor groove side would seriously disturb the active site, regardless of the presence and identity of dNTP. Furthermore, the simulations indicate that dATP and dTTP are better incorporated in the damaged system than in their respective mismatched but unmodified controls, suggesting that the PhIP adduct enhances incorporation of these mismatches. Finally, bulky C8-dG adducts, situated in the major groove, are likely to impede translocation in this polymerase (Rechkoblit et al. (2006), PLoS Biol., 4, e11). However, N2-dG adducts, which can reside on the minor groove side, appear to cause less hindrance when in this position.

Publication types

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

MeSH terms

  • Binding Sites
  • Carcinogens / chemistry
  • Computational Biology
  • Computer Simulation
  • DNA / chemistry
  • DNA Adducts / chemistry*
  • DNA Polymerase beta / chemistry*
  • DNA Polymerase beta / metabolism
  • Deoxyadenine Nucleotides / chemistry
  • Deoxyadenine Nucleotides / metabolism
  • Deoxycytosine Nucleotides / chemistry
  • Deoxycytosine Nucleotides / metabolism
  • Deoxyguanine Nucleotides / chemistry
  • Deoxyguanine Nucleotides / metabolism
  • Deoxyguanosine / analogs & derivatives*
  • Deoxyguanosine / chemistry
  • Deoxyribonucleotides / chemistry*
  • Deoxyribonucleotides / metabolism
  • Imidazoles / chemistry*
  • Models, Molecular*
  • Motion
  • Mutagenesis
  • Nucleic Acid Conformation
  • Sulfolobus solfataricus / enzymology
  • Thymine Nucleotides / chemistry
  • Thymine Nucleotides / metabolism


  • Carcinogens
  • DNA Adducts
  • Deoxyadenine Nucleotides
  • Deoxycytosine Nucleotides
  • Deoxyguanine Nucleotides
  • Deoxyribonucleotides
  • Imidazoles
  • Thymine Nucleotides
  • N-(deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine
  • 2'-deoxycytidine 5'-triphosphate
  • deoxyguanosine triphosphate
  • DNA
  • DNA Polymerase beta
  • Deoxyguanosine
  • 2'-deoxyadenosine triphosphate
  • thymidine 5'-triphosphate