Phase transition of DNA knotting in spherical space.

DNA knotting Monte Carlo simulation flexible kink model phase transition spherical confinement worm-like chain model

Journal

Journal of physics. Condensed matter : an Institute of Physics journal
ISSN: 1361-648X
Titre abrégé: J Phys Condens Matter
Pays: England
ID NLM: 101165248

Informations de publication

Date de publication:
22 07 2022
Historique:
received: 02 04 2022
accepted: 12 07 2022
pubmed: 13 7 2022
medline: 26 7 2022
entrez: 12 7 2022
Statut: epublish

Résumé

Knots have been discovered in various biological systems, such as DNA. The knotting probability of DNA in free space depends non-monotonically on its bending rigidity and has a prominent peak. The current work aims to understand the underlying mechanism of the non-monotonic dependence of DNA knotting probability on bending rigidity. Monte Carlo simulations are performed on a closed DNA molecule confined in spherical space described by a worm-like chain model and a flexible kink model, respectively. The closed DNA's contour length and the spherical space radius both increase knotting probability, but also alter the unimodal dependence of knotting probability on bending rigidity. This is generalized using universal phase diagrams based on the two models. Under the flexible kink model, the total knotting probability of closed DNA is obviously increased at a relatively high excited energy. This supports the expectation that the entropy effect of knot size favours knot formation at a relatively low bending rigidity. In a given spherical space, the increasing contour length of closed DNA described by the worm-like chain model results in a visible shift in the knotting probability distribution. At the same time, the gyration radius of non-trivial closed DNA becomes comparable to that of trivial closed DNA, so that their ratio is not anti-correlated with average knot length. For closed DNA of various contour lengths, the relationship between average knot length and bending rigidity has a universal behaviour: the average knot length decreases to a local minimum at a bending rigidity of ∼5 and then gradually increases to a constant value. The existence of the local minimum is determined by the cut-off distance in repulsive Lennard-Jones potential. The bending rigidity corresponding to the beginning of the constant average knot length is consistent with that at the peak in the knotting distribution. At this point, the knot-size effect balances with the fragment free-energy effect and, at an even greater bending rigidity, knot length breathes around the average knot length value.

Identifiants

pubmed: 35820412
doi: 10.1088/1361-648X/ac808f
doi:

Substances chimiques

DNA 9007-49-2

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

© 2022 IOP Publishing Ltd.

Auteurs

Xiaolin Nie (X)

School of Physics and Electronic Science, Guizhou Normal University, Guiyang 550025, People's Republic of China.
College of Physics, Guizhou University, Guiyang 550025, People's Republic of China.

Caiyun Xiong (C)

College of Physics, Guizhou University, Guiyang 550025, People's Republic of China.

Xun Zhou (X)

School of Physics and Electronic Science, Guizhou Normal University, Guiyang 550025, People's Republic of China.

Yanhui Liu (Y)

College of Physics, Guizhou University, Guiyang 550025, People's Republic of China.
Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, People's Republic of China.
Kechuang Industrial Development Company Limited, Gui'an New Area, Guiyang 550025, People's Republic of China.

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Classifications MeSH