ArticleNucleic acids research2024
Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 12 citations in OpenAlex.
- Chromosome topology gates productive RecA homology search.bioRxiv : the preprint server for biology · 2026Article
- Intercalation Favors DNA Covalent Photobinding in Photoresponsive Dual PDT/PCT Bimetallic Assemblies.Journal of chemical information and modeling · 2026Article
- Actively Induced Supercoiling Can Slow Down Plasmid Solutions by Trapping the Threading Entanglements.ACS nano · 2026Article
- Physical genomics: Why gene regulation is tug of war between polymer physics and biochemistry.Current opinion in structural biology · 2026Review
- The interplay between supercoiling and DNA modifying enzymes at the single-molecule level.Scientific reports · 2026Article
- CRISPR-Cas12a REC2-Nuc interactions drive target-strand cleavage and constrain trans cleavage.Nucleic acids research · 2025Article
- The effects of DMSO on DNA conformations and mechanics.Biophysical journal · 2025Article
- Future Directions of the Prokaryotic Chromosome Field.Molecular microbiology · 2025Article
- Single-molecule orientation-localization microscopy: Applications and approaches.Quarterly reviews of biophysics · 2024Review
- DNA supercoiling enhances DNA condensation by ParB proteins.Nucleic acids research · 2024Article
- Force-enhanced sensitive and specific detection of DNA-intercalative agents directly from microorganisms at single-molecule level.Nucleic acids research · 2024Article
- Single-molecule visualization of twin-supercoiled domains generated during transcription.Nucleic acids research · 2024Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
DNA stores our genetic information and is ubiquitous in applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and can change local DNA structure. Frequently, DNA occurs in closed topological forms where topology and supercoiling add a global constraint to the interplay of binding-induced deformations and strain-modulated binding. Here, we present a quantitative model with a straight-forward numerical implementation of how the global constraints introduced by DNA topology modulate binding. We focus on fluorescent intercalators, which unwind DNA and enable direct quantification via fluorescence detection. Our model correctly describes bulk experiments using plasmids with different starting topologies, different intercalators, and over a broad range of intercalator and DNA concentrations. We demonstrate and quantitatively model supercoiling-dependent binding in a single-molecule assay, where we directly observe the different intercalator densities going from supercoiled to nicked DNA. The single-molecule assay provides direct access to binding kinetics and DNA supercoil dynamics. Our model has broad implications for the detection and quantification of DNA, including the use of psoralen for UV-induced DNA crosslinking to quantify torsional tension in vivo, and for the modulation of DNA binding in cellular contexts.
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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.