Nonspecifically bound proteins spin while diffusing along DNA

Blainey, Paul C. ; Luo, Guobin ; Kou, S. C. ; Mangel, Walter F. ; Verdine, Gregory L. ; Bagchi, Biman ; Xie, X. Sunney (2009) Nonspecifically bound proteins spin while diffusing along DNA Nature Structural & Molecular Biology, 16 (12). pp. 1224-1229. ISSN 1545-9993

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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.

Item Type:Article
Source:Copyright of this article belongs to Nature Publishing Group.
ID Code:3962
Deposited On:13 Oct 2010 07:09
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