A mini-review of the diffusion dynamics of DNA-binding proteins: experiments and models

@article{Park2020AMO,
  title={A mini-review of the diffusion dynamics of DNA-binding proteins: experiments and models},
  author={Seongyun Park and O-Chul Lee and Xavier Durang and Jae-Hyung Jeon},
  journal={arXiv: Biological Physics},
  year={2020}
}
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet, investigations over recent decades have found that the diffusion dynamics of DNA-binding proteins are generally complicated and, further, protein-specific. In this review, we collect the experimental and theoretical studies that quantify the diffusion dynamics of DNA… 
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5 Citations
Background Citations
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5 Citations

DNA Flow-Stretch Assays for Studies of Protein-DNA Interactions at the Single-Molecule Level
TLDR
This review focuses on SM techniques employing surfaceimmobilized and relatively long DNA molecules for studying protein-DNA interaction mechanisms and shows many benefits for mechanistic target search studies of various DNA-binding proteins.
ATP Binding Facilitates Target Search of SWR1 Chromatin Remodeler by Promoting One-Dimensional Diffusion on DNA
TLDR
It is demonstrated that SWR1 has a kinetic binding preference for DNA of NDR length as opposed to gene-body linker length DNA, which is well characterized for DNA binding proteins.
Single-Molecule Microscopy Meets Molecular Dynamics Simulations for Characterizing the Molecular Action of Proteins on DNA and in Liquid Condensates
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  • Biology, Chemistry
    Frontiers in Molecular Biosciences
  • 2021
TLDR
The molecular action of DNA-binding proteins on DNA and in liquid condensate is discussed based on the latest studies that mainly focused on the model protein p53, e.g., molecular principles of uptake and dynamics in droplets.
Bayesian inference of Lévy walks via hidden Markov models
The Lévy walk (LW) is a non-Brownian random walk model that has been found to describe anomalous dynamic phenomena in diverse fields ranging from biology over quantum physics to ecology. Recurrently…
Bayesian inference of L\'evy walks via hidden Markov models
TLDR
A Markovian decomposition scheme to approximate a renewal process governed by a power-law waiting time distribution and it is demonstrated that the Bayesian method performs remarkably inferring the Lévy walk trajectories from given unclassified trajectory data set if the noise level is moderate.

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