ArticleNucleic acids research2012
DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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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
10 citing papers in PubMed.
- Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI.Nucleic acids research · 2023Article
- Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains.PLoS genetics · 2022Article
- Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- A novel arrangement of zinc finger nuclease system for in vivo targeted genome engineering: the tomato LEC1-LIKE4 gene case.Plant cell reports · 2016Article
- Optical Pushing: A Tool for Parallelized Biomolecule Manipulation.Biophysical journal · 2016Article
- Tethered fluorophore motion: studying large DNA conformational changes by single-fluorophore imaging.Biophysical journal · 2014Article
- Type II restriction endonucleases--a historical perspective and more.Nucleic acids research · 2014Review
- Organization of the BcgI restriction-modification protein for the cleavage of eight phosphodiester bonds in DNA.Nucleic acids research · 2013Article
- TALE-PvuII fusion proteins--novel tools for gene targeting.PloS one · 2013Article
- DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics.Nucleic acids research · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180° bend, while that with repeated sites has a convoluted 360° turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology.
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Registered trials
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