Figure 1.

Schemes for target site location. Three commonly discussed microscopic pathways for transferring a protein from one site to another along a long DNA molecule are ‘sliding’, ‘hopping’ and ‘intersegmental transfer’. (Top) A protein might ‘slide’ along the double helix, transferring from one base pair position to the adjacent one without dissociating from the DNA. Many repeated sliding events result in 1-D diffusion of the protein along the DNA contour. (Center) If dissociation occurs, the protein might re-encounter the same DNA, but at a new contour position: we term such an event a ‘hop’. (Bottom) On scales beyond the persistence length of the DNA double helix, 150 bp (50 nm), the DNA can run into itself as a result of its random thermally excited bending. Such encounters permit the protein to move from one DNA site to another via an intermediate in which the protein is bound transiently to both sites, a process called ‘intersegmental transfer’.