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Issue 6, 2011
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Physics of proteinDNA interactions: mechanisms of facilitated target search

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One of the most critical aspects of proteinDNA interactions is the ability of protein molecules to quickly find and recognize specific target sequences on DNA. Experimental measurements indicate that the corresponding association rates to few specific sites among large number of non-specific sites are typically large. For some proteins they might be even larger than maximal allowed three-dimensional diffusion rates. Although significant progress in understanding protein search and recognition of targets on DNA has been achieved, detailed mechanisms of these processes are still strongly debated. Here we present a critical review of current theoretical approaches and some experimental observations in this area. Specifically, the role of lowering dimensionality, non-specific interactions, diffusion along the DNA molecules, protein and target sites concentrations, and electrostatic effects are critically analyzed. Possible future directions and outstanding problems are also presented and discussed.

Graphical abstract: Physics of protein–DNA interactions: mechanisms of facilitated target search

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The article was received on 28 Sep 2010, accepted on 02 Nov 2010 and first published on 29 Nov 2010

Article type: Perspective
DOI: 10.1039/C0CP01966F
Phys. Chem. Chem. Phys., 2011,13, 2088-2095

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    Physics of proteinDNA interactions: mechanisms of facilitated target search

    A. B. Kolomeisky, Phys. Chem. Chem. Phys., 2011, 13, 2088
    DOI: 10.1039/C0CP01966F

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