How a protein searches for its specific site on DNA: The role of intersegment transfer

Tao Hu and B. I. Shklovskii
Phys. Rev. E 76, 051909 – Published 9 November 2007

Abstract

Proteins are known to locate their specific targets on DNA up to two orders of magnitude faster than predicted by the Smoluchowski three-dimensional diffusion rate. One of the mechanisms proposed to resolve this discrepancy is termed “intersegment transfer.” Many proteins have two DNA binding sites and can transfer from one DNA segment to another without dissociation to water. We calculate the target search rate for such proteins in a dense globular DNA, taking into account intersegment transfer working in conjunction with DNA motion and protein sliding along DNA. We show that intersegment transfer plays a very important role in cases where the protein spends most of its time adsorbed on DNA.

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  • Received 27 July 2007

DOI:https://doi.org/10.1103/PhysRevE.76.051909

©2007 American Physical Society

Authors & Affiliations

Tao Hu and B. I. Shklovskii

  • Theoretical Physics Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA

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Vol. 76, Iss. 5 — November 2007

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Physical Review E Scope Description to Include Biological Physics
January 14, 2016

The editors of Physical Review E are pleased to announce that the journal’s stated scope has been expanded to explicitly include the term “Biological Physics.”

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