ArticleNucleic acids research2012
Effective stiffening of DNA due to nematic ordering causes DNA molecules packed in phage capsids to preferentially form torus knots.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 56 citations in OpenAlex.
- Energy Landscapes of Model Knotted Polymers.Journal of chemical theory and computation · 2025Article
- Genome wide nucleosome landscape shapes 3D chromatin organization.Science advances · 2024Article
- AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins' Topology.Molecules (Basel, Switzerland) · 2023Article
- Biophysical ordering transitions underlie genome 3D re-organization during cricket spermiogenesis.Nature communications · 2023Article
- 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
- Ion-dependent DNA configuration in bacteriophage capsids.Biophysical journal · 2021Article
- Investigation of Ring and Star Polymers in Confined Geometries: Theory and Simulations.Entropy (Basel, Switzerland) · 2021Article
- Can Soft Models Describe Polymer Knots?Macromolecules · 2020Article
- A nanofluidic knot factory based on compression of single DNA in nanochannels.Nature communications · 2018Article
- Are There Knots in Chromosomes?Polymers · 2017Article
- Studies of global and local entanglements of individual protein chains using the concept of knotoids.Scientific reports · 2017Article
- Phage-like packing structures with mean field sequence dependence.Journal of computational chemistry · 2017Article
- Conformations and orientational ordering of semiflexible polymers in spherical confinement.The Journal of chemical physics · 2017Article
- Article
- Review
- A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains.PLoS computational biology · 2016Article
- LassoProt: server to analyze biopolymers with lassos.Nucleic acids research · 2016Article
- Article
Corrections and comments
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Authors and funding
4 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Observation that DNA molecules in bacteriophage capsids preferentially form torus type of knots provided a sensitive gauge to evaluate various models of DNA arrangement in phage heads. Only models resulting in a preponderance of torus knots could be considered as close to reality. Recent studies revealed that experimentally observed enrichment of torus knots can be qualitatively reproduced in numerical simulations that include a potential inducing nematic arrangement of tightly packed DNA molecules within phage capsids. Here, we investigate what aspects of the nematic arrangement are crucial for inducing formation of torus knots. Our results indicate that the effective stiffening of DNA by the nematic arrangement not only promotes knotting in general but is also the decisive factor in promoting formation of DNA torus knots in phage capsids.
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