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

Abstract
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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.

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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.
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.
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.
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.
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.

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