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

Reith D, Cifra P, Stasiak A, Virnau P - Nucleic Acids Res. (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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Related in: MedlinePlus

Effect of increasing stiffness on the overall shapes of polymer chains having the same length and being confined within a small sphere of the same diameter. (A) In case of fully flexible chains (B = 0), equilibrated configurations fill the available volume in a rather uniform way. (B), (C) and (D) present representative snapshots of polymer chains with increasing stiffness and having values of the parameter B amounting to 10, 20 and 45, respectively. Notice that as chains get stiffer they progressively adopt spool–like configurations with the centre being unoccupied. Whereas the configuration shown in (A) is unknotted, the remaining configurations are knotted. All snapshots show unanchored chains but anchored chains have very similar overall appearance.
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gks157-F1: Effect of increasing stiffness on the overall shapes of polymer chains having the same length and being confined within a small sphere of the same diameter. (A) In case of fully flexible chains (B = 0), equilibrated configurations fill the available volume in a rather uniform way. (B), (C) and (D) present representative snapshots of polymer chains with increasing stiffness and having values of the parameter B amounting to 10, 20 and 45, respectively. Notice that as chains get stiffer they progressively adopt spool–like configurations with the centre being unoccupied. Whereas the configuration shown in (A) is unknotted, the remaining configurations are knotted. All snapshots show unanchored chains but anchored chains have very similar overall appearance.

Mentions: Figure 1 shows overall shapes adopted by polymers with the same length but different stiffness when confined within a small sphere of the same diameter. We can see that highly flexible polymers fill the sphere of confinement in a rather uniform way (Figure 1A). However, as the stiffness of polymers increases they move toward the periphery of the sphere (Figure 1C and D). This result agrees with the intuitive expectation and an experiment that one could do in the lab by progressively feeding into a spherical distillation flask a long cotton string or a relatively stiff wire.Figure 1.


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

Reith D, Cifra P, Stasiak A, Virnau P - Nucleic Acids Res. (2012)

Effect of increasing stiffness on the overall shapes of polymer chains having the same length and being confined within a small sphere of the same diameter. (A) In case of fully flexible chains (B = 0), equilibrated configurations fill the available volume in a rather uniform way. (B), (C) and (D) present representative snapshots of polymer chains with increasing stiffness and having values of the parameter B amounting to 10, 20 and 45, respectively. Notice that as chains get stiffer they progressively adopt spool–like configurations with the centre being unoccupied. Whereas the configuration shown in (A) is unknotted, the remaining configurations are knotted. All snapshots show unanchored chains but anchored chains have very similar overall appearance.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3367193&req=5

gks157-F1: Effect of increasing stiffness on the overall shapes of polymer chains having the same length and being confined within a small sphere of the same diameter. (A) In case of fully flexible chains (B = 0), equilibrated configurations fill the available volume in a rather uniform way. (B), (C) and (D) present representative snapshots of polymer chains with increasing stiffness and having values of the parameter B amounting to 10, 20 and 45, respectively. Notice that as chains get stiffer they progressively adopt spool–like configurations with the centre being unoccupied. Whereas the configuration shown in (A) is unknotted, the remaining configurations are knotted. All snapshots show unanchored chains but anchored chains have very similar overall appearance.
Mentions: Figure 1 shows overall shapes adopted by polymers with the same length but different stiffness when confined within a small sphere of the same diameter. We can see that highly flexible polymers fill the sphere of confinement in a rather uniform way (Figure 1A). However, as the stiffness of polymers increases they move toward the periphery of the sphere (Figure 1C and D). This result agrees with the intuitive expectation and an experiment that one could do in the lab by progressively feeding into a spherical distillation flask a long cotton string or a relatively stiff wire.Figure 1.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: 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.

Show MeSH
Related in: MedlinePlus