ArticleBiophysical journal2008
Simulations of knotting in confined circular DNA.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Knot Formation on DNA Pushed Inside Chiral Nanochannels.Polymers · 2023Article
- Condensin minimizes topoisomerase II-mediated entanglements of DNA in vivo.The EMBO journal · 2021Article
- Chromatin Is Frequently Unknotted at the Megabase Scale.Biophysical journal · 2020Article
- Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA.Nucleic acids research · 2019Article
- The Rabl configuration limits topological entanglement of chromosomes in budding yeast.Scientific reports · 2019Article
- The exclusive effects of chaperonin on the behavior of proteins with 52 knot.PLoS computational biology · 2018Article
- DNA knots occur in intracellular chromatin.Nucleic acids research · 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
- Simulations of knotting of DNA during genome mapping.Biomicrofluidics · 2017Article
- Absence of knots in known RNA structures.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
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- Topological friction strongly affects viral DNA ejection.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Knotting of linear DNA in nano-slits and nano-channels: a numerical study.Journal of biological physics · 2013Article
- Dualities in the analysis of phage DNA packaging motors.Bacteriophage · 2012Article
- Effective stiffening of DNA due to nematic ordering causes DNA molecules packed in phage capsids to preferentially form torus knots.Nucleic acids research · 2012Article
- Role of DNA-DNA interactions on the structure and thermodynamics of bacteriophages Lambda and P4.Journal of structural biology · 2011Article
- Action at hooked or twisted-hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisomerases.Journal of molecular biology · 2010Article
- Knotted vs. unknotted proteins: evidence of knot-promoting loops.PLoS computational biology · 2010Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The packing of DNA inside bacteriophages arguably yields the simplest example of genome organization in living organisms. As an assay of packing geometry, the DNA knot spectrum produced upon release of viral DNA from the P4 phage capsid has been analyzed, and compared to results of simulation of knots in confined volumes. We present new results from extensive stochastic sampling of confined self-avoiding and semiflexible circular chains with volume exclusion. The physical parameters of the chains (contour length, cross section, and bending rigidity) have been set to match those of P4 bacteriophage DNA. By using advanced sampling techniques, involving multiple Markov chain pressure-driven confinement combined with a thermodynamic reweighting technique, we establish the knot spectrum of the circular chains for increasing confinement up to the highest densities for which available algorithms can exactly classify the knots. Compactified configurations have an enclosing hull diameter approximately 2.5 times larger than the P4 caliper size. The results are discussed in relation to the recent experiments on DNA knotting inside the capsid of a P4 tailless mutant. Our investigation indicates that confinement favors chiral knots over achiral ones, as found in the experiments. However, no significant bias of torus over twist knots is found, contrary to the P4 results. The result poses a crucial question for future studies of DNA packaging in P4: is the discrepancy due to the insufficient confinement of the equilibrium simulation or does it indicate that out-of-equilibrium mechanisms (such as rotation by packaging motors) affect the genome organization, hence its knot spectrum in P4?
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