ArticlePLoS computational biology2016
A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- Trefoil polymers from a knotted synthon.Nature chemistry · 2026Article
- Can Polymer Helicity Affect Topological Chirality of Polymer Knots?ACS macro letters · 2023Article
- Knot formation of dsDNA pushed inside a nanochannel.Scientific reports · 2022Article
- Influence of ionic conditions on knotting in a coarse-grained model for DNA.Frontiers in chemistry · 2022Article
- Can Soft Models Describe Polymer Knots?Macromolecules · 2020Article
- Stereoselective synthesis of a composite knot with nine crossings.Nature chemistry · 2018Article
- Are There Knots in Chromosomes?Polymers · 2017Article
- Pore translocation of knotted DNA rings.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Article
- Direct observation of DNA knots using a solid-state nanopore.Nature nanotechnology · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA chains exceeding 250,000 base pairs, assuming physiologically relevant salt conditions. The analysis is motivated by the emergence of DNA nanopore sequencing technology, as knots are a potential cause of erroneous nucleotide reads in nanopore sequencing devices and may severely limit read lengths in the foreseeable future. Even though our coarse-grained model is only based on experimental knotting probabilities of short DNA strands, it reproduces the correct persistence length of DNA. This indicates that knots are not only a fine gauge for structural properties, but a promising tool for the design of polymer models.
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Registered trials
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