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Nucleic Acids Res. 2012 Jun;40(11):5129-37. doi: 10.1093/nar/gks157. Epub 2012 Feb 22.

Effective stiffening of DNA due to nematic ordering causes DNA molecules packed in phage capsids to preferentially form torus knots.

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1
Institut für Physik, Johannes Gutenberg-Universität, 55128 Mainz, Germany.

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.

PMID:
22362732
PMCID:
PMC3367193
DOI:
10.1093/nar/gks157
[Indexed for MEDLINE]
Free PMC Article
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