ArticleNucleic acids research2018
Visualizing structure-mediated interactions in supercoiled DNA molecules.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 30 citations in OpenAlex.
- CRISPR RNA architecture steers Cas9 catalysis and fidelity via a guide repeat clasp motif.Nucleic acids research · 2026Article
- Stemless molecular beacon probes for single-molecule detection of supercoil-induced DNA denaturation.npj biological physics and mechanics · 2026Article
- A guide RNA repeat checkpoint steers CRISPR-Cas9 catalysis.bioRxiv : the preprint server for biology · 2025Article
- A high-throughput single-molecule platform to study DNA supercoiling effect on protein-DNA interactions.Nucleic acids research · 2025Article
- Fusions of Catalytically Inactive RusA to FokI Nuclease Coupled with PNA Enable Programmable Site-Specific Double-Stranded DNA Breaks.ACS omega · 2025Article
- Structural basis of Cas9 DNA interrogation with a 5' truncated sgRNA.Nucleic acids research · 2025Article
- Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo.International journal of molecular sciences · 2023Review
- Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β.Nature communications · 2022Article
- Article
- Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation.Nucleic acids research · 2022Article
- Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides.Nature communications · 2021Article
- Single-molecule visualization of the effects of ionic strength and crowding on structure-mediated interactions in supercoiled DNA molecules.Nucleic acids research · 2019Article
- Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling.Nucleic acids research · 2019Article
- Standalone interferometry-based calibration of convex lens-induced confinement microscopy with nanoscale accuracy.The Analyst · 2019Article
- Transcription factor regulation of RNA polymerase's torque generation capacity.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Miniaturized flow cell with pneumatically-actuated vertical nanoconfinement for single-molecule imaging and manipulation.Biomicrofluidics · 2018Article
Corrections and comments
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Authors and funding
13 authors at 3 institutions in 2 countries.
Funding
Abstract
We directly visualize the topology-mediated interactions between an unwinding site on a supercoiled DNA plasmid and a specific probe molecule designed to bind to this site, as a function of DNA supercoiling and temperature. The visualization relies on containing the DNA molecules within an enclosed array of glass nanopits using the Convex Lens-induced Confinement (CLiC) imaging method. This method traps molecules within the focal plane while excluding signal from out-of-focus probes. Simultaneously, the molecules can freely diffuse within the nanopits, allowing for accurate measurements of exchange rates, unlike other methods which could introduce an artifactual bias in measurements of binding kinetics. We demonstrate that the plasmid's structure influences the binding of the fluorescent probes to the unwinding site through the presence, or lack, of other secondary structures. With this method, we observe an increase in the binding rate of the fluorescent probe to the unwinding site with increasing temperature and negative supercoiling. This increase in binding is consistent with the results of our numerical simulations of the probability of site-unwinding. The temperature dependence of the binding rate has allowed us to distinguish the effects of competing higher order DNA structures, such as Z-DNA, in modulating local site-unwinding, and therefore binding.
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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.