The N-clasp of human DNA polymerase kappa promotes blockage or error-free bypass of adenine- or guanine-benzo[a]pyrenyl lesions

Nucleic Acids Res. 2008 Nov;36(20):6571-84. doi: 10.1093/nar/gkn719. Epub 2008 Oct 17.


DNA bypass polymerases are utilized to transit bulky DNA lesions during replication, but the process frequently causes mutations. The structural origins of mutagenic versus high fidelity replication in lesion bypass is therefore of fundamental interest. As model systems, we investigated the molecular basis of the experimentally observed essentially faithful bypass of the guanine 10S-(+)-trans-anti-benzo[a]pyrene-N(2)-dG adduct by the Y-family human DNA polymerase kappa, and the observed blockage of pol kappa produced by the adenine 10S-(+)-trans-anti-benzo[a]pyrene-N(2)-dA adduct. These lesions are derived from the most tumorigenic metabolite of the ubiquitous cancer-causing pollutant, benzo[a]pyrene. We compare our results for the dG adduct with our earlier studies for the pol kappa archaeal homolog Dpo4, which processes the same lesion in an error-prone manner. Molecular modeling, molecular mechanics calculations and molecular dynamics simulations were utilized. Our results show that the pol kappa N-clasp is a key structural feature that accounts for the dA adduct blockage and the near-error-free bypass of the dG lesion. Absence of the N-clasp in Dpo4 explains the error-prone processing of the same lesion by this enzyme. Thus, our studies elucidate structure-function relationships in the fidelity of lesion bypass.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Base Pairing
  • Benzopyrenes / chemistry*
  • Computer Simulation
  • DNA Adducts / chemistry*
  • DNA Damage*
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism
  • Deoxycytosine Nucleotides / chemistry
  • Deoxyguanosine / analogs & derivatives*
  • Deoxyguanosine / chemistry
  • Deoxyribonucleotides / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Sequence Alignment


  • Benzopyrenes
  • DNA Adducts
  • Deoxycytosine Nucleotides
  • Deoxyribonucleotides
  • anti-benzo(a)pyrene-dA adduct
  • benzo(a)pyrene N2-dG adduct
  • 2'-deoxycytidine 5'-triphosphate
  • DNA-Directed DNA Polymerase
  • POLK protein, human
  • Deoxyguanosine