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We develop revised theoretical ideas on the mechanism by which thetranscription factor proteins locate their specific binding sites on DNA fasterthan the three-dimensional (3D) diffusion controlled rate limit. We demonstratethat the 3D-diffusion controlled rate limit can be enhanced when the proteinmolecule reads several possible binding stretches of the template DNA viaone-dimensional (1D) diffusion upon each 3D-diffusion mediated collision ornonspecific binding event. The overall enhancement of site-specific associationrate is directly proportional to the maximum possible sliding length (LA,square root of (6Do/kr) where Do is the 1D-diffusion coefficient and kr is thedissociation rate constant associated with the nonspecific DNA-protein complex)associated with the 1D-diffusion of protein molecule along DNA. Uponconsidering several possible mechanisms we find that the DNA binding proteinscan efficiently locate their cognate sites on DNA by switching acrossfast-moving, slow-moving and reading states of their DNA binding domains in acyclic manner. Irrespective of the type of mechanism the overall rateenhancement factor asymptotically approaches a limiting value which is directlyproportional to LA as the total length of DNA that contains the cognate siteincreases. These results are consistent with the in vitro experimentalobservations.

Theory on the mechanism of rapid binding of transcription factor proteins at specific-sites on DNA