ArticleProceedings of the National Academy of Sciences of the United States of America2007
Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- CoNanoscale · 2025Article
- Short-range translocation by a restriction enzyme motor triggers diffusion along DNA.Nature chemical biology · 2024Article
- AFM Investigation of the Influence of Steam Flow through a Conical Coil Heat Exchanger on Enzyme Properties.Micromachines · 2022Article
- DNA Studies: Latest Spectroscopic and Structural Approaches.Micromachines · 2021Review
- DNA Manipulation and Single-Molecule Imaging.Molecules (Basel, Switzerland) · 2021Review
- Biological physics by high-speed atomic force microscopy.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2020Review
- Twist to disentangle.Nature structural & molecular biology · 2019Article
- [Progress in the applications of high-speed atomic force microscopy in cell biology].Nan fang yi ke da xue xue bao = Journal of Southern Medical University · 2018Review
- Single-site DNA cleavage by Type III restriction endonuclease requires a site-bound enzyme and a trans-acting enzyme that are ATPase-activated.Nucleic acids research · 2018Article
- High-speed atomic force microscopy imaging of live mammalian cells.Biophysics and physicobiology · 2017Review
- Chromosome Compaction by Active Loop Extrusion.Biophysical journal · 2016Article
- Re-evaluating the kinetics of ATP hydrolysis during initiation of DNA sliding by Type III restriction enzymes.Nucleic acids research · 2015Article
- Long-tip high-speed atomic force microscopy for nanometer-scale imaging in live cells.Scientific reports · 2015Article
- Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI.Scientific reports · 2014Article
- Type III restriction endonucleases are heterotrimeric: comprising one helicase-nuclease subunit and a dimeric methyltransferase that binds only one specific DNA.Nucleic acids research · 2014Article
- Filming biomolecular processes by high-speed atomic force microscopy.Chemical reviews · 2014Review
- Highlights of the DNA cutters: a short history of the restriction enzymes.Nucleic acids research · 2014Article
- Type III restriction-modification enzymes: a historical perspective.Nucleic acids research · 2014Review
- High-speed atomic force microscopy combined with inverted optical microscopy for studying cellular events.Scientific reports · 2013Article
- Dissociation from DNA of Type III Restriction-Modification enzymes during helicase-dependent motion and following endonuclease activity.Nucleic acids research · 2012Article
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8 authors.
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Abstract
Many DNA-modifying enzymes act in a manner that requires communication between two noncontiguous DNA sites. These sites can be brought into contact either by a diffusion-mediated chance interaction between enzymes bound at the two sites, or by active translocation of the intervening DNA by a site-bound enzyme. EcoP15I, a type III restriction enzyme, needs to interact with two recognition sites separated by up to 3,500 bp before it can cleave DNA. Here, we have studied the behavior of EcoP15I, using a novel fast-scan atomic force microscope, which uses a miniaturized cantilever and scan stage to reduce the mechanical response time of the cantilever and to prevent the onset of resonant motion at high scan speeds. With this instrument, we were able to achieve scan rates of up to 10 frames per s under fluid. The improved time resolution allowed us to image EcoP15I in real time at scan rates of 1-3 frames per s. EcoP15I translocated DNA in an ATP-dependent manner, at a rate of 79 +/- 33 bp/s. The accumulation of supercoiling, as a consequence of movement of EcoP15I along the DNA, could also be observed. EcoP15I bound to its recognition site was also seen to make nonspecific contacts with other DNA sites, thus forming DNA loops and reducing the distance between the two recognition sites. On the basis of our results, we conclude that EcoP15I uses two distinct mechanisms to communicate between two recognition sites: diffusive DNA loop formation and ATPase-driven translocation of the intervening DNA contour.
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