DNA polymerase bypass in vitro and in E. coli of a C-nucleotide analogue of Fapy-dG

Bioorg Med Chem. 2008 Apr 1;16(7):4029-34. doi: 10.1016/j.bmc.2008.01.025. Epub 2008 Jan 19.

Abstract

Bypass of the configurationally stable analogue (beta-C-Fapy x dG) of the formamidopyrimidine lesion derived from 2'-deoxyguanosine oxidation (Fapy x dG) was studied in vitro and in Escherichia coli. The exonuclease deficient Klenow fragment of E. coli DNA polymerase I (Klenow exo(-)) misincorporated dA most frequently opposite beta-C-Fapy x dG, but its efficiency was <0.2% of dC insertion. Klenow exo(-) fidelity was enhanced by the enzyme's high selectivity for extending duplexes only when dC was opposite beta-C-Fapy x dG. The expectations raised by these in vitro data were realized when beta-C-Fapy x dG replication was studied in E. coli by transfecting M13mp7(L2) bacteriophage DNA containing the nucleotide analogue within the lacZ gene in 4 local sequence contexts. The bypass efficiency of beta-C-Fapy x dG varied between 45% and 70% compared to a genome containing only native nucleotides. Mutation frequencies at the site of the lesions in the originally transfected genomes were determined using the REAP assay [Delaney, J. C.; Essigmann, J. M. Methods Enzymol.2006, 408, 1]. The levels of mutations could not be distinguished between those observed when genomes containing native nucleotides were replicated, indicating that the mutagenicity of beta-C-Fapy x dG was <1%. These data and previous reports indicate that beta-C-Fapy x dG is a good model of Fapy x dG in E. coli. In addition, these results and the previous report of beta-C-Fapy x dG binding to the base excision repair protein formamidopyrimidine glycosylase suggest that this analogue could be useful as a DNA repair inhibitor.

Publication types

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

MeSH terms

  • DNA Polymerase I / metabolism*
  • Escherichia coli / drug effects*
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Formamides / chemical synthesis*
  • Formamides / chemistry
  • Formamides / pharmacology*
  • Furans / chemical synthesis*
  • Furans / chemistry
  • Furans / pharmacology*
  • Genome, Bacterial / genetics
  • Kinetics
  • Molecular Sequence Data
  • Molecular Structure
  • Nucleotides / chemistry*
  • Pyrimidines / chemical synthesis*
  • Pyrimidines / chemistry
  • Pyrimidines / pharmacology*

Substances

  • Formamides
  • Furans
  • N6-(2-deoxy-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine
  • Nucleotides
  • Pyrimidines
  • DNA Polymerase I