Hopping, jumping and looping by restriction enzymes

Type II restriction endonucleases recognize specific DNA sequences and clea ve both strands of the DNA at fixed locations at or near their recognition sites. Many of these enzymes are dimeric proteins that recognize, in symmet rical fashion, palindromic DNA sequences. They generally catalyse independe nt reactions at each recognition site on the DNA, although in some cases th ey act processively; cutting the DNA first at one site, then translocating along the DNA to another site and cutting that before leaving the DNA. The way in which the degree of processivity varies with the length of DNA betwe en the sites can reveal the mechanism of translocation. In contrast with th e common view that proteins move along DNA by 'sliding', the principal mode of transfer of the EcoRV endonuclease is by 'hopping' and 'jumping', i.e. the dissociation of the protein from one site followed by its re-associatio n with another site in the same DNA molecule, either close to or distant fr om the original site. Other type II restriction enzymes require two copies of their recognition sites for their DNA cleavage reactions. Many of these enzymes, such as SfiI, are tetramers with two DNA-binding surfaces. SfiI ha s no activity when bound to just one recognition site, and instead both DNA -binding surfaces have to be filled before it becomes active. Although the two sites can be on separate DNA molecules, SfiI acts optimally with two si tes on the same DNA, where it traps the DNA between the sites in a loop. Sf iI thus constitutes a test system for the analysis of DNA looping.