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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.

SUBMITTER: Wang L

PROVIDER: S-EPMC3763527 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature

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Probing DNA clamps with single-molecule force spectroscopy.

Wang Lin L Xu Xiaojun X Kumar Ravindra R Maiti Buddhadev B Liu C Tony CT Ivanov Ivaylo I Lee Tae-Hee TH Benkovic Stephen J SJ

Nucleic acids research 20130619 16

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 wi ...[more]

PMID: 23783571

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