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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

Coaxially spooled inflection-free configurations are more difficult to attain for twist knots such as 41 and 52 than for torus knots such as 31 and 51.
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gks157-F5: Coaxially spooled inflection-free configurations are more difficult to attain for twist knots such as 41 and 52 than for torus knots such as 31 and 51.

Mentions: Studies investigating relative frequencies with which various types of DNA knots formed in bacteriophage capsids revealed that these knots have a much different spectrum as compared to knots formed randomly. For example, while freely fluctuating polymers in free space (17,18) or random trajectories highly confined to a sphere (8) result about twice more frequently in formation of five crossing twist knots (with the standard mathematical notation 52) than of five crossing torus knots (51) (see Figure 5 for schematic presentations of these knots) the opposite is the case for DNA knots formed in phage capsids (8). The standard mathematical notations of knots such as 52 use two numbers where the first one, written with normal fonts, indicates the minimal number of crossings a given knot type can have in a projection whereas the subscript number indicates the tabular position of a given knot type among the knots with the same minimal crossing number in standard tables of knots. Another ‘anomaly’ of knots formed in phage heads concerns the four crossing knot 41 (see Figure 5). That type of knots due to its relative simplicity forms much more frequently than five crossing torus knots (51) or five crossing twist knots (52) by random trajectories in confined volumes (8) or by DNA knots formed in free solution (19,20). However, among knots formed in phage capsids knot 41 is found strongly underrepresented and forms significantly less frequently than 51 or 52 knots (8).


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)

Coaxially spooled inflection-free configurations are more difficult to attain for twist knots such as 41 and 52 than for torus knots such as 31 and 51.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gks157-F5: Coaxially spooled inflection-free configurations are more difficult to attain for twist knots such as 41 and 52 than for torus knots such as 31 and 51.
Mentions: Studies investigating relative frequencies with which various types of DNA knots formed in bacteriophage capsids revealed that these knots have a much different spectrum as compared to knots formed randomly. For example, while freely fluctuating polymers in free space (17,18) or random trajectories highly confined to a sphere (8) result about twice more frequently in formation of five crossing twist knots (with the standard mathematical notation 52) than of five crossing torus knots (51) (see Figure 5 for schematic presentations of these knots) the opposite is the case for DNA knots formed in phage capsids (8). The standard mathematical notations of knots such as 52 use two numbers where the first one, written with normal fonts, indicates the minimal number of crossings a given knot type can have in a projection whereas the subscript number indicates the tabular position of a given knot type among the knots with the same minimal crossing number in standard tables of knots. Another ‘anomaly’ of knots formed in phage heads concerns the four crossing knot 41 (see Figure 5). That type of knots due to its relative simplicity forms much more frequently than five crossing torus knots (51) or five crossing twist knots (52) by random trajectories in confined volumes (8) or by DNA knots formed in free solution (19,20). However, among knots formed in phage capsids knot 41 is found strongly underrepresented and forms significantly less frequently than 51 or 52 knots (8).

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