Abstract
SSB proteins bind to and control the accessibility of single-stranded (ss) DNA generated as a transient intermediate during a variety of cellular processes. For subsequent DNA processing, however, SSB needs to be removed and yield to other proteins while avoiding ssDNA exposure to nucleases. Using single-molecule two- and three-color fluorescence resonance energy transfer (FRET) and fluorescence-force spectroscopy, we recently showed that the SSB/DNA complex is a highly dynamic system and SSB functions as a sliding platform that migrates on ssDNA for recruiting other proteins in DNA repair, replication, and recombination. Here, we present the activity assays in detail for observing the transitions between different SSB binding modes and SSB diffusion on ssDNA in real time by using single-molecule FRET microscopy and for studying how mechanical forces regulate SSB–DNA interactions using fluorescence-force spectroscopy. These single-molecule approaches are generally applicable to many other protein–nucleic acid systems.
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Acknowledgements
We thank all the members of Ha laboratory for experimental help and discussions. These studies were supported by grants from the National Institutes of Health (RR025341 and GM065367) and the National Science Foundation (0822613 and 0646550). TH is an employee of the Howard Hughes Medical Institute.
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Zhou, R., Ha, T. (2012). Single-Molecule Analysis of SSB Dynamics on Single-Stranded DNA. In: Keck, J. (eds) Single-Stranded DNA Binding Proteins. Methods in Molecular Biology, vol 922. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-032-8_5
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DOI: https://doi.org/10.1007/978-1-62703-032-8_5
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