One- and three-dimensional pathways for proteins to reach specific DNA sites

Proteins that interact with specific DNA sites bind to DNA at random and th en translocate to the target site. This may occur by one-dimensional diffus ion along the DNA, or through three-dimensional space via multiple dissocia tion/re-associations. To distinguish these routes, reactions of the EcoRV e ndonuclease were studied on substrates with two EcoRV sites separated by va ried distances. The fraction of encounters between the DNA and the protein that resulted in the processive cleavage of both sites decreased as the len gth of intervening DNA was increased, but not in the manner demanded for on e-dimensional diffusion. The variation in processivity with inter-site spac ing shows instead that protein moves from one site to another through three -dimensional space, by successive dissociation/re-associations, though each re-association to a new site is followed by a search of the DNA immediatel y adjacent to that site. Although DNA-binding proteins are usually thought to find their target sites by one-dimensional pathways, three-dimensional r outes may be more common than previously anticipated.