Kinetics of Protein-DNA Interactions: First-Passage Analysis

All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of investigating dynamics of protein-DNA interactions, which govern al...

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Bibliographic Details
Published inarXiv.org
Main Authors Kochugaeva, Maria P, Shvets, Alexey A, Kolomeisky, Anatoly B
Format Paper
LanguageEnglish
Published Ithaca Cornell University Library, arXiv.org 26.04.2018
Subjects
Binding sites
Biological activity
Deoxyribonucleic acid
DNA
Organic chemistry
Proteins
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Summary:All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of investigating dynamics of protein-DNA interactions, which govern all major biological processes. It is based on a first-passage analysis of biochemical and biophysical transitions, and it provides a fully analytic description of the processes. Our approach is explained for the case of a single protein searching for a specific binding site on DNA. In addition, the application of the method to investigations of the effect of DNA sequence heterogeneity, and the role multiple targets and traps in the protein search dynamics are discussed.
ISSN:2331-8422