title: DNA concentration-dependent dissociation of EcoRI: direct transfer or reaction during hopping.
abstract: Direct transfer of proteins between DNA helices is a recognized important feature of the recognition site search process. Direct transfer is characterized by a dissociation rate that depends on total DNA concentration. This is taken as evidence for the formation of an intermediate DNA-protein-DNA ternary complex. We find that the dissociation rate of EcoRI-DNA-specific complexes at 80 mM NaCl depends on the concentration of competitor oligonucleotide suggesting that direct transfer contributes to EcoRI dissociation. This dependence on competitor DNA concentration is not seen at 180 mM salt. A careful examination of the salt concentration dependence of the dissociation rate, however, shows that the predictions for the formation of a ternary complex are not observed experimentally. The findings can be rationalized by considering that just after dissociating from a DNA fragment the protein remains in close proximity to that fragment, can reassociate with it, and diffuse back to the recognition site rather than bind to an oligonucleotide in solution, a hopping excursion. The probability that a protein will bind to an oligonucleotide during a hop can be approximately calculated and shown to explain the data. A dependence of the dissociation rate of a DNA-protein complex on competitor DNA concentration does not necessarily mean direct transfer.
authors.affiliation: The Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Nina Y
authors.initials: NY
authors.lastname: Sidorova
authors.forename: Thomas
authors.initials: T
authors.lastname: Scott
authors.forename: Donald C
authors.initials: DC
authors.lastname: Rau
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D015246:Deoxyribonuclease EcoRI / Q000378:metabolism*; D007700:Kinetics; D009838:Oligodeoxyribonucleotides / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding / Q000187:drug effects; D012965:Sodium Chloride / Q000494:pharmacology
chemical_list: D009838:Oligodeoxyribonucleotides; D012965:Sodium Chloride; D004247:DNA; D015246:Deoxyribonuclease EcoRI