ArticlePhysical review. E, Statistical, nonlinear, and soft matter physics2011
Protein sliding and hopping kinetics on DNA.
Article in Physical review. E, Statistical, nonlinear, and soft matter physics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Decoding the base flipping mechanism of the SET- and RING-associated (SRA) domain of the epigenetic UHRF1 protein.Nucleic acids research · 2025Article
- Conformational Change of Transcription Factors from Search to Specific Binding: AThe journal of physical chemistry. B · 2022Article
- Probability of Immobilization on Host Cell Surface Regulates Viral Infectivity.Physical review letters · 2020Article
- The Role of Noncognate Sites in the 1D Search Mechanism of EcoRI.Biophysical journal · 2019Article
- Facilitated diffusion buffers noise in gene expression.Physical review. E, Statistical, nonlinear, and soft matter physics · 2014Article
- Microscopic mechanism of DNA damage searching by hOGG1.Nucleic acids research · 2014Article
- Article
- DNA concentration-dependent dissociation of EcoRI: direct transfer or reaction during hopping.Biophysical journal · 2013Article
- Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level.International journal of molecular sciences · 2013Article
- Computational models for large-scale simulations of facilitated diffusion.Molecular bioSystems · 2012Review
- A comprehensive computational model of facilitated diffusion in prokaryotes.Bioinformatics (Oxford, England) · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Using Monte Carlo simulations, we deconvolved the sliding and hopping kinetics of GFP-LacI proteins on elongated DNA from their experimentally observed seconds-long diffusion trajectories. Our simulations suggest the following results: (i) in each diffusion trajectory, a protein makes on average hundreds of alternating slides and hops with a mean sliding time of several tens of milliseconds; (ii) sliding dominates the root-mean-square displacement of fast diffusion trajectories, whereas hopping dominates slow ones; (iii) flow and variations in salt concentration have limited effects on hopping kinetics, while in vivo DNA configuration is not expected to influence sliding kinetics; and (iv) the rate of occurrence for hops longer than 200 nm agrees with experimental data for EcoRV proteins.
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Registered trials
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