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

Junji Iwahara, Anatoly B. Kolomeisky

Research output: Contribution to journalReview articlepeer-review

Abstract

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.

Original languageEnglish (US)
Article number106521
JournalBiophysical Chemistry
Volume269
DOIs
StatePublished - Feb 2021

Keywords

  • Diffusion
  • Dynamics
  • Kinetics
  • Protein-DNA interactions
  • Target search

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Organic Chemistry

Fingerprint Dive into the research topics of 'Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications'. Together they form a unique fingerprint.

Cite this