ArticleNucleic acids research2008
Dynamics and consequences of DNA looping by the FokI restriction endonuclease.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
11 citing papers in PubMed, 25 citations in OpenAlex.
- Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI.Nucleic acids research · 2023Article
- Type II restriction endonucleases--a historical perspective and more.Nucleic acids research · 2014Review
- TstI, a Type II restriction-modification protein with DNA recognition, cleavage and methylation functions in a single polypeptide.Nucleic acids research · 2014Article
- Characterization of cleavage intermediate and star sites of RM.Tth111II.Scientific reports · 2014Article
- DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.Nucleic acids research · 2012Article
- DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations.Nucleic acids research · 2012Article
- Related bifunctional restriction endonuclease-methyltransferase triplets: TspDTI, Tth111II/TthHB27I and TsoI with distinct specificities.BMC molecular biology · 2012Article
- Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer.Nucleic acids research · 2012Article
- Unlinking of supercoiled DNA catenanes by type IIA topoisomerases.Biophysical journal · 2011Article
- Simulation of DNA catenanes.Physical chemistry chemical physics : PCCP · 2009Review
- Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands.Nucleic acids research · 2009Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Genetic events often require proteins to be activated by interacting with two DNA sites, trapping the intervening DNA in a loop. While much is known about looping equilibria, only a few studies have examined DNA-looping dynamics experimentally. The restriction enzymes that cut DNA after interacting with two recognition sites, such as FokI, can be used to exemplify looping reactions. The reaction pathway for FokI on a supercoiled DNA with two sites was dissected by fast kinetics to reveal, in turn: the initial binding of a protein monomer to each site; the protein-protein association to form the dimer, trapping the loop; the subsequent phosphodiester hydrolysis step. The DNA motion that juxtaposes the sites ought on the basis of Brownian dynamics to take approximately 2 ms, but loop capture by FokI took 230 ms. Hence, DNA looping by FokI is rate limited by protein association rather than DNA dynamics. The FokI endonuclease also illustrated activation by looping: it cut looped DNA 400 times faster than unlooped DNA.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.