Discrete Persistent Chain Model for Protein Binding on DNA

Details Discrete Persistent Chain Model for Protein Binding on DNA Discrete Persistent Chain Model for Protein Binding on DNA

2011-04-19

arxiv.org/abs/1104.3836v1

Physical Review E83, 041912 (2011)

Physics

Condensed Matter

Statistical Mechanics

14 pages, 5 figures

Scientific paper

We describe and solve a discrete persistent chain model of protein binding on DNA, involving an extra sigma_i s at a site i of the DNA. This variable takes the value 1 or 0 depending on whether the site is occupied by a protein or not. In addition, if the site is occupied by a protein, there is an extra energy cost epsilon. For small force, we obtain analytic expressions for the force-extension curve and the fraction of bound protein on the DNA.For higher forces, the model can be solved numerically to obtain force extension curves and the average fraction of bound proteins as a function of applied force. Our model can be used to analyze experimental force extension curves of protein binding on DNA, and hence deduce the number of bound proteins in the case of non-specific binding.

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