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

DOI10.1142/S0129183109014023MaRDI QIDQ3394719zbMATH OpenWikidataFDO

Authors Debanjan Chowdhury

Publication date 8 September 2009

Published in International Journal of Modern Physics C (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0708.1931

zbMATH Keywords

first passage timesMonte-Carlo simulationself-avoiding walk

Mathematics Subject Classification ID

Random walks, random surfaces, lattice animals, etc. in equilibrium statistical mechanics (82B41) Statistical mechanics of polymers (82D60) Cell biology (92C37)

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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Cited in

(8)

• Modeling promoter search by \textit{E. coli} RNA polymerase: one-dimensional diffusion in a sequence-dependent energy landscape
• How conformational dynamics influences the protein search for targets on DNA
• On the ion-mediated interaction between protein and DNA
• Generalized theory on the mechanism of site-specific DNA-protein interactions
• First-passage processes on a filamentous track in a dense traffic: optimizing diffusive search for a target in crowding conditions
• How a protein searches for its site on DNA: the mechanism of facilitated diffusion
• Target search of a protein on DNA in the presence of position-dependent bias
• The search for a DNA target in the nucleus

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