Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: a 5'-slippage mechanism

Biochemistry. 2008 Mar 4;47(9):2701-9. doi: 10.1021/bi701839q. Epub 2008 Feb 9.

Abstract

The Y-family DNA polymerase Dpo4, from the archaeon bacterium Sulfolobus solfataricus, is a member of the DinB family, which also contains human Pol kappa. It has a spacious active site that can accommodate two templating bases simultaneously, with one of them skipped by the incoming dNTP. Assays of single dNTP insertion opposite a benzo[ a]pyrene-derived N (2)-dG adduct, 10 S(+)- trans- anti-[BP]- N (2)-dG ([BP]G*), reveal that an incoming dATP is significantly preferred over the other three dNTPs in the TG 1*G 2 sequence context. Molecular modeling and dynamics simulations were carried out to interpret this experimental observation on a molecular level. Modeling studies suggest that the significant preference for dATP insertion observed experimentally can result from two possible dATP incorporation modes. The dATP can be inserted opposite the T on the 5' side of the adduct G 1*, using an unusual 5'-slippage pattern, in which the unadducted G 2, rather than G 1*, is skipped, to produce a -1 deletion. In addition, the dATP can be misincorporated opposite the adduct. The 5'-slippage pattern may be generally facilitated in cases where the base 3' to the lesion is the same as the adducted base.

Publication types

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

MeSH terms

  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / metabolism
  • Base Pairing
  • Base Sequence
  • Benzopyrenes / chemistry*
  • Benzopyrenes / metabolism
  • Binding Sites
  • Computer Simulation
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / metabolism
  • Deoxyadenine Nucleotides / chemistry
  • Deoxyadenine Nucleotides / metabolism
  • Deoxyguanosine / analogs & derivatives*
  • Deoxyguanosine / chemistry
  • Deoxyguanosine / metabolism
  • Models, Molecular
  • Molecular Structure
  • Nucleotides / chemistry*
  • Nucleotides / metabolism
  • Substrate Specificity
  • Sulfolobus solfataricus / enzymology
  • Sulfolobus solfataricus / metabolism

Substances

  • Archaeal Proteins
  • Benzopyrenes
  • Deoxyadenine Nucleotides
  • Nucleotides
  • benzo(a)pyrene N2-dG adduct
  • DNA-Directed DNA Polymerase
  • Deoxyguanosine
  • 2'-deoxyadenosine triphosphate