ArticleBiochemistry2009
Single-molecule dynamics of the DNA-EcoRII protein complexes revealed with high-speed atomic force microscopy.
Article in Biochemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed, 81 citations in OpenAlex.
- Advances in scanning probe microscopy for biological systems.Biophysics reports · 2026Article
- Visualizing and Quantifying microRNA-Induced DNA Origami Separation at the Nanoscale.Angewandte Chemie (International ed. in English) · 2026Article
- Assembly of Synaptic Protein-DNA Complexes: Critical Role of Non-Specific Interactions.International journal of molecular sciences · 2023Article
- Open-source controller for low-cost and high-speed atomic force microscopy imaging of skin corneocyte nanotextures.HardwareX · 2022Article
- Tools shaping drug discovery and development.Biophysics reviews · 2022Review
- Site-Search Process for Synaptic Protein-DNA Complexes.International journal of molecular sciences · 2021Article
- Characterize the Interaction of the DNA Helicase PriA with the Stalled DNA Replication Fork Using Atomic Force Microscopy.Bio-protocol · 2021Article
- 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
- Probing The Structure And Dynamics Of Nucleosomes Using Atomic Force Microscopy Imaging.Journal of visualized experiments : JoVE · 2019Article
- A model for the evolution of prokaryotic DNA restriction-modification systems based upon the structural malleability of Type I restriction-modification enzymes.Nucleic acids research · 2018Article
- [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
- Dynamics of the Interaction of RecG Protein with Stalled Replication Forks.Biochemistry · 2018Article
- Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes.Journal of physics D: Applied physics · 2018Article
- Optimal Length of Conformational Transition Region in Protein Search for Targets on DNA.The journal of physical chemistry letters · 2017Article
- 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
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
The study of interactions of protein with DNA is important for gaining a fundamental understanding of how numerous biological processes occur, including recombination, transcription, repair, etc. In this study, we use the EcoRII restriction enzyme, which employs a three-site binding mechanism to catalyze cleavage of a single recognition site. Using high-speed atomic force microscopy (HS-AFM) to image single-molecule interactions in real time, we were able to observe binding, translocation, and dissociation mechanisms of the EcoRII protein. The results show that the protein can translocate along DNA to search for the specific binding site. Also, once specifically bound at a single site, the protein is capable of translocating along the DNA to locate the second specific binding site. Furthermore, two alternative modes of dissociation of the EcoRII protein from the loop structure were observed, which result in the protein stably bound as monomers to two sites or bound to a single site as a dimer. From these observations, we propose a model in which this pathway is involved in the formation and dynamics of a catalytically active three-site complex.
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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.