ArticleThe European physical journal. E, Soft matter2011
The diffusion constant of a labeled protein sliding along DNA.
Article in The European physical journal. E, Soft matter, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA.Nucleic acids research · 2017Article
- Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions.Nature communications · 2016Article
- Single molecule studies of DNA mismatch repair.DNA repair · 2014Review
- TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres.Nucleic acids research · 2014Article
- Nascent RNA structure modulates the transcriptional dynamics of RNA polymerases.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- The rotation-coupled sliding of EcoRV.Nucleic acids research · 2012Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long ago inferred by biochemists, the linear diffusion of proteins along DNA has recently been observed at a single-molecule level using fluorescence microscopy. This imaging technique requires labeling the protein of interest with a fluorophore, usually an organic nanosized dye that is not supposed to impact the dynamics of the protein. Yet individual proteins can also be tracked using much larger labels, like quantum dots or beads. We investigate here the impact of such a large label on the protein diffusion along DNA. Solving a Fokker-Planck equation, we estimate the diffusion constant of a protein-label complex diffusing in a periodic potential that mimics the DNA-protein interaction, the link between the protein and the label being modeled as a Hookean spring. Our results indicate that the diffusion constant can generally be calculated by considering that the motion of the protein in the DNA potential is decoupled from the Brownian motion of the label. Our conclusions are in good agreement with the experimental results we obtained with the restriction enzyme EcoRV, assuming a rotation-coupled diffusion of the enzyme along DNA.
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