Probing DNA clamps with single-molecule force spectroscopy

Lin Wang, Xiaojun Xu, Ravindra Kumar, Buddhadev Maiti, C. Tony Liu, Ivaylo Ivanov, Tae Hee Lee, Stephen J. Benkovic

Research output: Contribution to journalArticle

9 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)7804-7814
Number of pages11
JournalNucleic acids research
Volume41
Issue number16
DOIs
StatePublished - Sep 1 2013

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Molecular Dynamics Simulation
Mechanics
Saccharomyces cerevisiae
Optical Tweezers
Escherichia coli
DNA
Single Molecule Imaging

All Science Journal Classification (ASJC) codes

  • Genetics

Cite this

Wang, L., Xu, X., Kumar, R., Maiti, B., Liu, C. T., Ivanov, I., ... Benkovic, S. J. (2013). Probing DNA clamps with single-molecule force spectroscopy. Nucleic acids research, 41(16), 7804-7814. https://doi.org/10.1093/nar/gkt487
Wang, Lin ; Xu, Xiaojun ; Kumar, Ravindra ; Maiti, Buddhadev ; Liu, C. Tony ; Ivanov, Ivaylo ; Lee, Tae Hee ; Benkovic, Stephen J. / Probing DNA clamps with single-molecule force spectroscopy. In: Nucleic acids research. 2013 ; Vol. 41, No. 16. pp. 7804-7814.
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Wang, L, Xu, X, Kumar, R, Maiti, B, Liu, CT, Ivanov, I, Lee, TH & Benkovic, SJ 2013, 'Probing DNA clamps with single-molecule force spectroscopy', Nucleic acids research, vol. 41, no. 16, pp. 7804-7814. https://doi.org/10.1093/nar/gkt487

Probing DNA clamps with single-molecule force spectroscopy. / Wang, Lin; Xu, Xiaojun; Kumar, Ravindra; Maiti, Buddhadev; Liu, C. Tony; Ivanov, Ivaylo; Lee, Tae Hee; Benkovic, Stephen J.

In: Nucleic acids research, Vol. 41, No. 16, 01.09.2013, p. 7804-7814.

Research output: Contribution to journalArticle

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Wang L, Xu X, Kumar R, Maiti B, Liu CT, Ivanov I et al. Probing DNA clamps with single-molecule force spectroscopy. Nucleic acids research. 2013 Sep 1;41(16):7804-7814. https://doi.org/10.1093/nar/gkt487