Binding of specific DNA base-pair mismatches by N-methylpurine-DNA glycosylase and its implication in initial damage recognition

Tapan Biswas, Lawrence J. Clos, John SantaLucia, Sankar Mitra, Rabindra Roy

Research output: Contribution to journalArticle

23 Scopus citations

Abstract

Most DNA glycosylases including N-methylpurine-DNA glycosylase (MPG), which initiate DNA base excision repair, have a wide substrate range of damaged or altered bases in duplex DNA. In contrast, uracil-DNA glycosylase (UDG) is specific for uracil and excises it from both single-stranded and duplex DNAs. Here we show by DNA footprinting analysis that MPG, but not UDG, bound to base-pair mismatches especially to less stable pyrimidine-pyrimidine pairs, without catalyzing detectable base cleavage. Thermal denaturation studies of these normal and damaged (e.g. 1,N6-ethenoadenine, εA) base mispairs indicate that duplex instability rather than exact fit of the flipped out damaged base in the catalytic pocket is a major determinant in the initial recognition of damage by MPG. Finally, based on our determination of binding affinity and catalytic efficiency we conclude that the initial recognition of substrate base lesions by MPG is dependent on the ease of flipping of the base from unstable pairs to a flexible catalytic pocket.

Original languageEnglish (US)
Pages (from-to)503-513
Number of pages11
JournalJournal of Molecular Biology
Volume320
Issue number3
DOIs
StatePublished - 2002

Keywords

  • Catalytic efficiency
  • DNA instability
  • Mismatch
  • N-methylpurine-DNA glycosylase
  • Substrate recognition

ASJC Scopus subject areas

  • Virology

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