ArticleNucleic acids research2018
Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking.
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 9 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
9 citing papers in PubMed, 30 citations in OpenAlex.
- Single-molecule magnetic tweezers reveal distinct dynamics and enhanced mechanical stability of ssDNA 31 and 52 knots.Nucleic acids research · 2026Article
- Article
- Geometric Predictors of Knotted and Linked Arcs.ACS polymers Au · 2022Article
- A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.Frontiers in molecular biosciences · 2021Review
- Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches.Nucleic acids research · 2020Article
- Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure.Nucleic acids research · 2020Article
- Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA.Nucleic acids research · 2019Article
- A multiscale analysis of DNA phase separation: from atomistic to mesoscale level.Nucleic acids research · 2019Article
- Kinetic pathways of topology simplification by Type-II topoisomerases in knotted supercoiled DNA.Nucleic acids research · 2019Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Knots and supercoiling are both introduced in bacterial plasmids by catalytic processes involving DNA strand passages. While the effects on plasmid organization has been extensively studied for knotting and supercoiling taken separately, much less is known about their concurrent action. Here, we use molecular dynamics simulations and oxDNA, an accurate mesoscopic DNA model, to study the kinetic and metric changes introduced by complex (five-crossing) knots and supercoiling in 2 kbp-long DNA rings. We find several unexpected results. First, the conformational ensemble is dominated by two distinct states, differing in branchedness and knot size. Secondly, fluctuations between these states are as fast as the metric relaxation of unknotted rings. In spite of this, certain boundaries of knotted and plectonemically-wound regions can persist over much longer timescales. These pinned regions involve multiple strands that are interlocked by the cooperative action of topological and supercoiling constraints. Their long-lived character may be relevant for the simplifying action of topoisomerases.
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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.