ArticleProceedings of the National Academy of Sciences of the United States of America2013
Topological friction strongly affects viral DNA ejection.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Generating knotted polymer and protein structures by machine learning.Communications chemistry · 2026Article
- A parallel algorithm for the computation of the Jones polynomial.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Alexidine, identified as a Z-DNA inducer by the NanoZ screening platform, acts as a transcriptional regulator.Nucleic acids research · 2026Article
- Single-molecule magnetic tweezers reveal distinct dynamics and enhanced mechanical stability of ssDNA 31 and 52 knots.Nucleic acids research · 2026Article
- Polymer sailing on rafts within lipid membranes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins' Topology.Molecules (Basel, Switzerland) · 2023Article
- Role of DNA-DNA sliding friction and nonequilibrium dynamics in viral genome ejection and packaging.Nucleic acids research · 2023Article
- Knot Factories with Helical Geometry Enhance Knotting and Induce Handedness to Knots.Polymers · 2022Article
- Knot formation of dsDNA pushed inside a nanochannel.Scientific reports · 2022Article
- A ravel alliance.Nature chemistry · 2021Article
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- Complex DNA knots detected with a nanopore sensor.Nature communications · 2019Article
- Stereoselective synthesis of a composite knot with nine crossings.Nature chemistry · 2018Article
- Dynamics of supercoiled DNA with complex knots: large-scale rearrangements and persistent multi-strand interlocking.Nucleic acids research · 2018Article
- KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.The European physical journal. E, Soft matter · 2018Article
- Are There Knots in Chromosomes?Polymers · 2017Article
- Compaction of quasi-one-dimensional elastoplastic materials.Nature communications · 2017Article
- Conformations and orientational ordering of semiflexible polymers in spherical confinement.The Journal of chemical physics · 2017Article
- Pore translocation of knotted DNA rings.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
Corrections and comments
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Bacteriophages initiate infection by releasing their double-stranded DNA into the cytosol of their bacterial host. However, what controls and sets the timescales of DNA ejection? Here we provide evidence from stochastic simulations which shows that the topology and organization of DNA packed inside the capsid plays a key role in determining these properties. Even with similar osmotic pressure pushing out the DNA, we find that spatially ordered DNA spools have a much lower effective friction than disordered entangled states. Such spools are only found when the tendency of nearby DNA strands to align locally is accounted for. This topological or conformational friction also depends on DNA knot type in the packing geometry and slows down or arrests the ejection of twist knots and very complex knots. We also find that the family of (2, 2k+1) torus knots unravel gradually by simplifying their topology in a stepwise fashion. Finally, an analysis of DNA trajectories inside the capsid shows that the knots formed throughout the ejection process mirror those found in gel electrophoresis experiments for viral DNA molecules extracted from the capsids.
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