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Originally published as Biophys J. BioFAST on May 20, 2005.
doi:10.1529/biophysj.104.057612
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Biophysical Journal 89:895-902 (2005)
© 2005 The Biophysical Society

Target Search of N Sliding Proteins on a DNA

Igor M. Sokolov *, Ralf Metzler {dagger}, Kiran Pant {ddagger} and Mark C. Williams {ddagger}

* Institut für Physik, Humboldt Universität zu Berlin, Berlin, Germany; {dagger} NORDITA—Nordic Institute for Theoretical Physics, Copenhagen, Denmark; and {ddagger} Department of Physics, Northeastern University, Boston, Massachusetts

Correspondence: Address reprint requests to R. Metzler, Tel.: 45-35-325507; E-mail: metz{at}nordita.dk.

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.




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