Nonspecifically bound proteins spin while diffusing along DNA
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 k{sub B}T. Such small barriers facilitate rapid search for binding sites.
- Research Organization:
- Brookhaven National Lab. (BNL), Upton, NY (United States)
- Sponsoring Organization:
- NATIONAL INSTITUTE OF HEALTH
- DOE Contract Number:
- DE-AC02-98CH10886
- OSTI ID:
- 1040362
- Report Number(s):
- BNL-90688-2010-JA; 400412000; TRN: US201210%%539
- Journal Information:
- Nature Structural and Molecular Biology, Vol. 16, Issue 12
- Country of Publication:
- United States
- Language:
- English
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