ArticleBiophysical journal2011
Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Review
- Assembly of Synaptic Protein-DNA Complexes: Critical Role of Non-Specific Interactions.International journal of molecular sciences · 2023Article
- Tools shaping drug discovery and development.Biophysics reviews · 2022Review
- Site-Search Process for Synaptic Protein-DNA Complexes.International journal of molecular sciences · 2021Article
- Observing Protein One-Dimensional Sliding: Methodology and Biological Significance.Biomolecules · 2021Review
- Viral RNA recognition by LGP2 and MDA5, and activation of signaling through step-by-step conformational changes.Nucleic acids research · 2020Article
- Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging.Journal of visualized experiments : JoVE · 2019Article
- Visualization of conformational variability in the domains of long single-stranded RNA molecules.Nucleic acids research · 2017Article
- Imaging of DNA and Protein-DNA Complexes with Atomic Force Microscopy.Critical reviews in eukaryotic gene expression · 2016Review
- Filming biomolecular processes by high-speed atomic force microscopy.Chemical reviews · 2014Review
- Visualization of DNA and protein-DNA complexes with atomic force microscopy.Methods in molecular biology (Clifton, N.J.) · 2014Article
- Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame.Nucleic acids research · 2013Article
- High-speed atomic force microscopy combined with inverted optical microscopy for studying cellular events.Scientific reports · 2013Article
- Article
- Guide to video recording of structure dynamics and dynamic processes of proteins by high-speed atomic force microscopy.Nature protocols · 2012Article
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Authors and funding
6 authors.
Funding
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Abstract
Many DNA regulatory factors require communication between distantly separated DNA sites for their activity. The type IIF restriction enzyme SfiI is often used as a model system of site communication. Here, we used fast-scanning atomic force microscopy to monitor the DNA cleavage process with SfiI and the changes in the single SfiI-DNA complex in the presence of either Mg²⁺ or Ca²⁺ at a scan rate of 1-2 fps. The increased time resolution allowed us to visualize the concerted cleavage of the protein at two cognate sites. The four termini generated by the cleavage were released in a multistep manner. The high temporal resolution enabled us to visualize the translocation of a DNA strand on a looped complex and intersegmental transfer of the SfiI protein in which swapping of the site is performed without protein dissociation. On the basis of our results, we propose that the SfiI tetramer can remain bound to one of the sites even after cleavage, allowing the other site on the DNA molecule to fill the empty DNA-binding cleft by combining a one-dimensional diffusion-mediated sliding and a segment transfer mechanism.
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