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Searching For Targets On A Model Dna: Effects Of Inter-Segment Hopping, Detachment, And Re-Attachment

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  • DEBANJAN CHOWDHURY

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

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.

Suggested Citation

  • Debanjan Chowdhury, 2009. "Searching For Targets On A Model Dna: Effects Of Inter-Segment Hopping, Detachment, And Re-Attachment," International Journal of Modern Physics C (IJMPC), World Scientific Publishing Co. Pte. Ltd., vol. 20(06), pages 817-830.
    • Handle: RePEc:wsi:ijmpcx:v:20:y:2009:i:06:n:s0129183109014023
    DOI: 10.1142/S0129183109014023
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    1. van Damme, E.E.C., 2008. "Eerlijk spel," Other publications TiSEM 0c961413-226b-4091-8f8a-1, Tilburg University, School of Economics and Management.
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