How do proteins search for their specific sites on coiled or globular DNA

Details How do proteins search for their specific sites on coiled or globular DNA How do proteins search for their specific sites on coiled or globular DNA

2005-10-24

arxiv.org/abs/q-bio/0510043v1

Biophysical Journal, v. 90, p. 2731-2744, 2006

Biology

Quantitative Biology

Biomolecules

16 pages, 5 figures

Scientific paper

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 3D diffusion rate. It was the idea due to Delbruck that they are non-specifically adsorbed on DNA, and sliding along DNA provides for the faster 1D search. Surprisingly, the role of DNA conformation was never considered in this context. In this article, we explicitly address the relative role of 3D diffusion and 1D sliding along coiled or globular DNA and the possibility of correlated re-adsorbtion 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 in some regimes to dramatic deceleration of the reaction.

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