title: How proteins search for their specific sites on DNA: the role of DNA conformation.
abstract: It is known since the early days of molecular biology that proteins locate their specific targets on DNA up to two orders-of-magnitude faster than the Smoluchowski three-dimensional diffusion rate. An accepted explanation of this fact is that proteins are nonspecifically adsorbed on DNA, and sliding along DNA provides for the faster one-dimensional search. Surprisingly, the role of DNA conformation was never considered in this context. In this article, we explicitly address the relative role of three-dimensional diffusion and one-dimensional sliding along coiled or globular DNA and the possibility of correlated readsorption of desorbed proteins. We have identified a wealth of new different scaling regimes. We also found the maximal possible acceleration of the reaction due to sliding. We found that the maximum on the rate-versus-ionic strength curve is asymmetric, and that sliding can lead not only to acceleration, but also in some regimes to dramatic deceleration of the reaction.
authors.affiliation: Department of Physics, and William I. Fine Theoretical Physics Institute, University of Minnesota, Minneapolis, USA.
authors.forename: Tao
authors.initials: T
authors.lastname: Hu
authors.forename: A Yu
authors.initials: AY
authors.lastname: Grosberg
authors.forename: B I
authors.initials: BI
authors.lastname: Shklovskii
mesh_terms: D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D055672:Static Electricity; D014867:Water / Q000737:chemistry
chemical_list: D004268:DNA-Binding Proteins; D014867:Water; D004247:DNA