Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease

Rapid-reaction methods have been used previously to identify intermediates in the reaction of the EcoRV restriction endonuclease on oligonucleotide substrates. In this study, the pathway on macromolecular DNA was elucidated by using the quench-flow method to analyze EcoRV reactions on a plasmid with one recognition site. Some reactions were carried out by first allowing the EcoRV enzyme to bind nonspecifically to the DNA and then initiating DNA cleavage by adding magnesium ions. The subsequent transfer of the enzyme from nonspecific to specific sites was extremely rapid, at a random walk rate of at least 5 x 10(5) base pairs per second. The two strands of the DNA at the EcoRV recognition site were then cleaved sequentially, at rates that were faster than the turnover number of the enzyme. The rates recorded for the cleavage steps were direct measurements of phosphodiester hydrolysis, while the turnover is limited by the dissociation of the product cleaved in both strands. Other reactions were initiated by adding EcoRV and MgCl2 to the DNA: these revealed not only the processes observed in reactions starting from DNA-bound enzyme but also the bimolecular association of the protein with the plasmid. The association rate was limited by diffusion but its rate constant, 1.2 x 10(8) M-1 s(-1), was unusually small for the binding of a protein to DNA. The slowness of this diffusion-controlled process may be due to a rapid oscillation of the protein between closed and open conformations, with only the open form capable of binding DNA.