SEARCHING FOR TARGETS ON A MODEL DNA: EFFECTS OF INTER-SEGMENT HOPPING, DETACHMENT, AND RE-ATTACHMENT

Debanjan Chowdhury ()
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Debanjan Chowdhury: Department of Physics, Indian Institute of Technology, Kanpur 208016, India

International Journal of Modern Physics C (IJMPC), 2009, vol. 20, issue 06, 817-830

Abstract: For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base-pairs while the DNA is usually several millions of base-pairs long. How does the protein search for the target site? What is the most efficient mechanism for a successful search? Motivated by these fundamental questions on intracellular biological processes, we have developed a model for searching a specific site on a model DNA by a single protein. We have made a comparative quantitative study on the efficiencies of sliding, inter-segmental hoppings and detachment/re-attachments of the particle during its search for the specific site on the DNA. We also introduce some new quantitative measures ofefficiencyof a search process by defining a relevant quantity, which can be measured inin-vitroexperiments.

Keywords: Self-avoiding walk; Monte-Carlo simulation; first passage times; 87.16.af; 87.10.Rt (search for similar items in EconPapers)
Date: 2009
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DOI: 10.1142/S0129183109014023

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