Probing DNA clamps with single-molecule force spectroscopy

Nucleic Acids Res. 2013 Sep;41(16):7804-14. doi: 10.1093/nar/gkt487. Epub 2013 Jun 19.

Abstract

Detailed mechanisms of DNA clamps in prokaryotic and eukaryotic systems were investigated by probing their mechanics with single-molecule force spectroscopy. Specifically, the mechanical forces required for the Escherichia coli and Saccharomyces cerevisiae clamp opening were measured at the single-molecule level by optical tweezers. Steered molecular dynamics simulations further examined the forces involved in DNA clamp opening from the perspective of the interface binding energies associated with the clamp opening processes. In combination with additional molecular dynamics simulations, we identified the contact networks between the clamp subunits that contribute significantly to the interface stability of the S.cerevisiae and E. coli clamps. These studies provide a vivid picture of the mechanics and energy landscape of clamp opening and reveal how the prokaryotic and eukaryotic clamps function through different mechanisms.

Publication types

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

MeSH terms

  • DNA Polymerase III / chemistry*
  • Escherichia coli Proteins / chemistry*
  • Molecular Dynamics Simulation
  • Optical Tweezers
  • Proliferating Cell Nuclear Antigen / chemistry*
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Spectrum Analysis / methods

Substances

  • Escherichia coli Proteins
  • Proliferating Cell Nuclear Antigen
  • Saccharomyces cerevisiae Proteins
  • beta subunit, DNA polymerase III
  • DNA Polymerase III