Target search on DNA -- effect of coiling
Preprint
Abstract
Some proteins can find their targets on DNA faster than by pure diffusion in the 3-dimensional cytoplasm, through the process of facilitated diffusion: They can loosely bind to DNA and temporarily slide along it, thus being guided by the DNA molecule itself to the target. This chapter examines this process in mathematical detail with a focus on including the effect of DNA coiling on the search process.Keywords
All Related Versions
This publication has 31 references indexed in Scilit:
- Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysisThe Journal of Chemical Physics, 2018
- Real sequence effects on the search dynamics of transcription factors on DNAScientific Reports, 2015
- Probing short-range protein Brownian motion in the cytoplasm of living cellsNature Communications, 2014
- Facilitated diffusion with DNA coilingProceedings of the National Academy of Sciences, 2009
- How DNA coiling enhances target localization by proteinsProceedings of the National Academy of Sciences, 2008
- Mechanical Measurement of Single-molecule Binding Rates: Kinetics of DNA Helix-destabilization by T4 Gene 32 ProteinJournal of Molecular Biology, 2004
- Specificity, free energy and information content in protein–DNA interactionsTrends in Biochemical Sciences, 1998
- Facilitated Target Location in Biological SystemsJournal of Biological Chemistry, 1989
- Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theoryBiochemistry, 1981
- Association kinetics with coupled diffusion. An extension to coiled-chain macromolecules applied to the LAC repressor-operator systemBiophysical Chemistry, 1977