Abstract
It is known that DNA-binding proteins can slide along the DNA helix while searching for specific binding sites, but their path of motion remains obscure. Do these proteins undergo simple one-dimensional (1D) translational diffusion, or do they rotate to maintain a specific orientation with respect to the DNA helix? We measured 1D diffusion constants as a function of protein size while maintaining the DNA-protein interface. Using bootstrap analysis of single-molecule diffusion data, we compared the results to theoretical predictions for pure translational motion and rotation-coupled sliding along the DNA. The data indicate that DNA-binding proteins undergo rotation-coupled sliding along the DNA helix and can be described by a model of diffusion along the DNA helix on a rugged free-energy landscape. A similar analysis including the 1D diffusion constants of eight proteins of varying size shows that rotation-coupled sliding is a general phenomenon. The average free-energy barrier for sliding along the DNA was 1.1 ± 0.2 kBT. Such small barriers facilitate rapid search for binding sites.
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Acknowledgements
We would like to thank Y. Qi (Harvard Univ.) for providing labeled E. coli MutM, W.J. McGrath and V. Graziano (Brookhaven Natl. Lab.) for a gift of labeled AVP-pVIc, and E.S. Vanamee and A. Aggarwal (Mount Sinai School of Medicine) for a gift of labeled BamHI. We also thank G.W. Li and J. Elf for contributing LacI-Venus diffusion data. B.B. was supported partly by a grant from DST (India) and by a JC Bose Fellowship. Work at Harvard was funded by the NIH Director's Pioneer Award and by NSF.
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Blainey, P., Luo, G., Kou, S. et al. Nonspecifically bound proteins spin while diffusing along DNA. Nat Struct Mol Biol 16, 1224–1229 (2009). https://doi.org/10.1038/nsmb.1716
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DOI: https://doi.org/10.1038/nsmb.1716
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