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Biophys. J. BioFAST: First Published May 20, 2005. doi:10.1529/biophysj.104.057612
© 2005 by the Biophysical Society.

A more recent version of this article appeared on August 1, 2005.
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BIOPHYSICAL THEORY AND MODELING

Target search of N sliding proteins on a DNA

Igor M Sokolov 1, Ralf Metzler 2*, Kiran Pant 3 and Mark C. Williams 3

1 Humboldt University Berlin
2 Nordita
3 Northeastern University

* To whom correspondence should be addressed. E-mail: metz{at}nordita.dk.

Submitted on December 6, 2004
Revised on February 28, 2005
Accepted on 9 May 2005


  Abstract
At low to moderate ambient salt concentrations, DNA-binding proteins bind relatively tightly to DNA, and only very rarely detach. Intersegmental transfer due to DNA-looping can be excluded by applying an external pulling force to the DNA molecule. Under such conditions, we explore the targeting dynamics of N proteins sliding diffusively along DNA in search of their specific target sequence. At lower densities of binding proteins, we find a reduction of the characteristic search time proportional to N^{-2}, with corrections at higher concentrations. Rates for detachment and attachment of binding proteins are incorporated in the model. Our findings are in agreement with recent single molecule studies in the presence of bacteriophage T4 gene 32 protein for which the unbinding rate is much lower than the specific binding rate.

Key Words: Berg-von Hippel model, Binding proteins, DNA, Dynamics of target sequence search, First passage time, Gene regulation




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Copyright © 2005 by the Biophysical Society.