1. Structural Biology and Molecular Biophysics
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Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways

  1. Sukrit Suksombat
  2. Rustem Khafizov
  3. Alexander G Kozlov
  4. Timothy M Lohman
  5. Yann R Chemla  Is a corresponding author
  1. University of Illinois at Urbana-Champaign, United States
  2. Washington University School of Medicine, United States
Research Article
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Cite this article as: eLife 2015;4:e08193 doi: 10.7554/eLife.08193

Abstract

Escherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologies remain speculative. Here, we used single-molecule force and fluorescence spectroscopy to investigate E. coli SSB binding to ssDNA. Stretching a single ssDNA-SSB complex reveals discrete states that correlate with known binding modes, the likely ssDNA conformations and diffusion dynamics in each, and the kinetic pathways by which the protein wraps ssDNA and is dissociated. The data allow us to construct an energy landscape for the ssDNA-SSB complex, revealing that unwrapping energy costs increase the more ssDNA is unraveled. Our findings provide insights into the mechanism by which proteins gain access to ssDNA bound by SSB, as demonstrated by experiments in which SSB is displaced by the E. coli recombinase RecA.

Article and author information

Author details

  1. Sukrit Suksombat

    Department of Physics, Center for the Physics of Living Cells, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Rustem Khafizov

    Department of Physics, Center for the Physics of Living Cells, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Alexander G Kozlov

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Timothy M Lohman

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Yann R Chemla

    Department of Physics, Center for the Physics of Living Cells, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States
    For correspondence
    ychemla@illinois.edu
    Competing interests
    The authors declare that no competing interests exist.

Reviewing Editor

  1. John Kuriyan, Howard Hughes Medical Institute, University of California, Berkeley, United States

Publication history

  1. Received: April 21, 2015
  2. Accepted: August 24, 2015
  3. Accepted Manuscript published: August 25, 2015 (version 1)
  4. Version of Record published: September 25, 2015 (version 2)

Copyright

© 2015, Suksombat et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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