Quantifying length-dependent DNA end-binding by nucleoproteins

Vo, Thi-Dieu-Hien; Albrecht, Amanda V.; Wilson, W. David; Poon, Gregory M.K.

doi:10.1016/j.bpc.2019.106177

Cited by 2 publications

(1 citation statement)

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“…Because electrostatic interactions are crucial for protein-DNA association [ 70 ], the kinetics and thermodynamics of protein-DNA interactions strongly depend on the salt concentration used in experiments [ 29 , 34 , 64 , 67 , 83 – 88 ]. The counterion condensation theory predicts a linear relationship between log K d and log[salt] for the dissociation constants of protein-DNA complexes [ 85 , 86 ] and a similar linear relationship between log k and log[salt] for some kinetic rate constants relevant to protein-DNA constants [ 89 ].…”

Section: Experimental Applicationsmentioning

confidence: 99%

Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications

Iwahara

Kolomeisky

2021

Biophysical Chemistry

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To perform their functions, transcription factors and DNA-repair/modifying enzymes randomly search DNA in order to locate their specific targets on DNA. Discrete-state stochastic kinetic models have been developed to explain how the efficiency of the search process is influenced by the molecular properties of proteins and DNA as well as by other factors such as molecular crowding. These theoretical models not only offer explanations on the relation of microscopic processes to macroscopic behavior of proteins, but also facilitate the analysis and interpretation of experimental data. In this review article, we provide an overview on discrete-state stochastic kinetic models and explain how these models can be applied to experimental investigations using stopped-flow, single-molecule, nuclear magnetic resonance (NMR), and other biophysical and biochemical methods.

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