ArticleProceedings of the National Academy of Sciences of the United States of America2017
Pore translocation of knotted DNA rings.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Coarse-Graining Reshapes Knot Dynamics in Polymers and Proteins.The journal of physical chemistry. B · 2026Article
- Generating knotted polymer and protein structures by machine learning.Communications chemistry · 2026Article
- Single-molecule magnetic tweezers reveal distinct dynamics and enhanced mechanical stability of ssDNA 31 and 52 knots.Nucleic acids research · 2026Article
- Effects of Knotting on the Collapse of Active Ring Polymers.Macromolecules · 2025Article
- Unzipping of knotted DNA via nanopore translocation.QRB discovery · 2025Article
- Activity-driven polymer knotting for macromolecular topology engineering.Science advances · 2024Article
- Constraints on Knot Insertion, Not Internal Jamming, Control Polycatenane Translocation Dynamics through Crystalline Pores.Macromolecules · 2023Article
- Driven translocation of a semiflexible polymer through a conical channel in the presence of attractive surface interactions.Scientific reports · 2022Article
- Geometric Predictors of Knotted and Linked Arcs.ACS polymers Au · 2022Article
- Article
- Knot formation of dsDNA pushed inside a nanochannel.Scientific reports · 2022Article
- Topological Friction and Relaxation Dynamics of Spatially Confined Catenated Polymers.ACS macro letters · 2022Article
- Influence of ionic conditions on knotting in a coarse-grained model for DNA.Frontiers in chemistry · 2022Article
- Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures.Polymers · 2021Article
- Structure-flexible DNA origami translocation through a solid-state nanopore.RSC advances · 2021Article
- RNA Pore Translocation with Static and Periodic Forces: Effect of Secondary and Tertiary Elements on Process Activation and Duration.The journal of physical chemistry. B · 2021Article
- Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches.Nucleic acids research · 2020Article
- Article
- Directional translocation resistance of Zika xrRNA.Nature communications · 2020Article
- Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure.Nucleic acids research · 2020Article
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Authors and funding
2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We use an accurate coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translocation of 10-kbp-long DNA rings that are knotted. By monitoring various topological and physical observables we find that there is not one, as previously assumed, but rather two qualitatively different modes of knot translocation. For both modes the pore obstruction caused by knot passage has a brief duration and typically occurs at a late translocation stage. Both effects are well in agreement with experiments and can be rationalized with a transparent model based on the concurrent tensioning and sliding of the translocating knotted chains. We also observed that the duration of the pore obstruction event is more controlled by the knot translocation velocity than the knot size. These features should advance the interpretation and design of future experiments aimed at probing the spontaneous knotting of biopolymers.
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