Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution

Proc Natl Acad Sci U S A. 2009 Dec 15;106(50):21109-14. doi: 10.1073/pnas.0908640106. Epub 2009 Dec 2.

Abstract

The catalytic mechanism of DNA polymerases involves multiple steps that precede and follow the transfer of a nucleotide to the 3'-hydroxyl of the growing DNA chain. Here we report a single-molecule approach to monitor the movement of E. coli DNA polymerase I (Klenow fragment) on a DNA template during DNA synthesis with single base-pair resolution. As each nucleotide is incorporated, the single-molecule Förster resonance energy transfer intensity drops in discrete steps to values consistent with single-nucleotide incorporations. Purines and pyrimidines are incorporated with comparable rates. A mismatched primer/template junction exhibits dynamics consistent with the primer moving into the exonuclease domain, which was used to determine the fraction of primer-termini bound to the exonuclease and polymerase sites. Most interestingly, we observe a structural change after the incorporation of a correctly paired nucleotide, consistent with transient movement of the polymerase past the preinsertion site or a conformational change in the polymerase. This may represent a previously unobserved step in the mechanism of DNA synthesis that could be part of the proofreading process.

Publication types

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

MeSH terms

  • Base Pairing*
  • Catalysis
  • DNA Polymerase I / metabolism*
  • Escherichia coli Proteins / genetics
  • Fluorescence Resonance Energy Transfer*
  • Kinetics
  • Methods
  • Motion
  • Nucleotides / metabolism*
  • Templates, Genetic

Substances

  • Escherichia coli Proteins
  • Nucleotides
  • DNA Polymerase I