Expanding the Repertoire of DNA Polymerase Substrates: Template-Instructed Incorporation of Non-Nucleoside Triphosphate Analogues by DNA Polymerases Beta and Lambda

Nucleic Acids Res. 2007;35(1):45-57. doi: 10.1093/nar/gkl1016. Epub 2006 Dec 5.

Abstract

We have recently shown that neither the base nor the sugar moieties of a nucleotide is an essential feature for its incorporation by DNA polymerases (pols) lambda and beta. Here we present the identification of novel non-nucleoside triphosphate (NNTP) derivatives belonging to three classes: (i) non-substrate-specific inhibitors of DNA pol lambda; (ii) substrate inhibitors which could preferentially be incorporated by either DNA pol lambda wild type or its Y505A mutant and (iii) the substrate inhibitor N-(Biphenylcarbonyl)-4-oxobutyl triphosphate which could be incorporated exclusively by DNA pol beta in a Mg2+-dependent manner, and preferentially pairs with A on the template. This compound represents the first example of a substrate lacking both nucleobase and ribose residue, showing distinct base-pairing properties with normal bases. Therefore, this NNTP analog can be considered as the prototype of an entirely novel class of DNA pol substrates.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Pairing
  • DNA Nucleotidylexotransferase / metabolism
  • DNA Polymerase beta / genetics
  • DNA Polymerase beta / metabolism*
  • DNA-Directed DNA Polymerase / metabolism
  • Enzyme Inhibitors / chemistry
  • Humans
  • Magnesium / chemistry
  • Manganese / chemistry
  • Mutation
  • Nucleosides / chemistry
  • Organophosphates / chemistry*
  • Organophosphates / metabolism
  • Substrate Specificity
  • Templates, Genetic
  • Tyrosine / genetics

Substances

  • Enzyme Inhibitors
  • N-(biphenylcarboxyl)-4-oxobutyl triphosphate
  • Nucleosides
  • Organophosphates
  • Tyrosine
  • Manganese
  • DNA Polymerase beta
  • DNA polymerase X
  • DNA polymerase beta2
  • DNA Nucleotidylexotransferase
  • DNA-Directed DNA Polymerase
  • Magnesium