Single-Molecule Dynamics of the DNA-EcoRII Protein Complexes Revealed with High-Speed Atomic Force Microscopy

The study of interactions of protein with DNA is important for gaining a fundamental understanding of how numerous biological processes occur, including recombination, transcription, repair. etc In tills study, we use the EcoRII restriction enzyme, which employs it three-site binding mechanism to catalyze eleavage of a single recognition site Using high-speed atomic force microscopy (HS-AFM) to image single-molecule interactions ill real time, we were able to observe binding, translocation, and dissociation mechanisms of the EcoRII protein. The results show that the protein call translocate along DNA to search for the specific binding site. Also. once specifically bound at it single site, the protein is capable of translocating along the DNA to locate the second specific binding site. Furthermore, two alternative modes of dissociation of the EcoRII protein from the loop structure were observed, which result Ill the protein stably bound as monomers to two sites or bound to a single Site as it duller. From these observations, we propose a model in which this pathway is involved in the formation and dynamics of a catalytically active three-site complex