How proteins search for their specific sites on DNA: the role of DNA conformation.
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.
Hu
Tao
T
Department of Physics, and William I. Fine Theoretical Physics Institute, University of Minnesota, Minneapolis, USA.
Grosberg
A Yu
AY
Shklovskii
B I
BI
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
D004268:DNA-Binding Proteins; D014867:Water; D004247:DNA