Mechanisms of Diffusional Search of Specific Targets by DNA-Dependent Proteins (review)
To perform their functions, many DNA-dependent proteins have to quickly locate specific targets against a vast excess of nonspecific DNA. Although this problem was posed over 40 years ago, the mechanism of such search remains an incompletely solved problem in the field of protein-DNA interactions. Several, not mutually exclusive mechanisms have been suggested: sliding, involving one-dimensional random diffusion along the DNA contour; hopping, in which the protein moves between closely spaced DNA fragments; macroscopic association-dissociation of the protein-DNA complex; and intersegmental transfer. This review covers the modern state of the problem of target DNA search, including theoretical descriptions and methods of study of this process at the macroscopic level (molecule ensembles) and at the microscopic level (individual molecules). Almost all studied DNA-dependent proteins search for specific targets by combined three-dimensional diffusion and one-dimensional diffusion along the DNA contour.