title: Probing DNA clamps with single-molecule force spectroscopy.
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.
authors.affiliation: Department of Chemistry, the Pennsylvania State University, University Park, PA 16802, USA and Department of Chemistry, Georgia State University, Atlanta, GA 30302, USA.
authors.forename: Lin
authors.initials: L
authors.lastname: Wang
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Xu
authors.forename: Ravindra
authors.initials: R
authors.lastname: Kumar
authors.forename: Buddhadev
authors.initials: B
authors.lastname: Maiti
authors.forename: C Tony
authors.initials: CT
authors.lastname: Liu
authors.forename: Ivaylo
authors.initials: I
authors.lastname: Ivanov
authors.forename: Tae-Hee
authors.initials: TH
authors.lastname: Lee
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: Benkovic
mesh_terms: D004258:DNA Polymerase III / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D052898:Optical Tweezers; D018809:Proliferating Cell Nuclear Antigen / Q000737:chemistry*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry*; D013057:Spectrum Analysis / Q000379:methods
chemical_list: D029968:Escherichia coli Proteins; D018809:Proliferating Cell Nuclear Antigen; D029701:Saccharomyces cerevisiae Proteins; C101139:beta subunit, DNA polymerase III; D004258:DNA Polymerase III