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

Cornell Affiliated Author(s)

Author

Debanjan Chowdhury

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 of efficiency of a search process by defining a relevant quantity, which can be measured in in-vitro experiments. © 2009 World Scientific Publishing Company.

Date Published

Journal

International Journal of Modern Physics C

Volume

20

Issue

6

Number of Pages

817-830,

URL

https://www.scopus.com/inward/record.uri?eid=2-s2.0-68249153282&doi=10.1142%2fS0129183109014023&partnerID=40&md5=e01ebf7f5df8f0b0e6c453fbd9ab55be

DOI

10.1142/S0129183109014023

Group (Lab)

Debanjan Chowdhury Group

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