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arXiv · 0708.1931

Searching for targets on a model DNA: Effects of inter-segment hopping, detachment and re-attachment

Debanjan Chowdhury
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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 of 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 of {\it efficiency} of a search process by defining a relevant quantity, which can be measured in {\it in-vitro} experiments.

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BibTeXRIS

Debanjan Chowdhury. 2010-01-10. Searching for targets on a model DNA: Effects of inter-segment hopping, detachment and re-attachment. https://doi.org/10.1142/s0129183109014023

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