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Condensed Matter > Soft Condensed Matter
Title: Influence of ionic conditions on knotting in a coarse-grained model for DNA
(Submitted on 14 Nov 2022 (v1), last revised 23 Dec 2022 (this version, v2))
Abstract: We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers. We find that the occurrence of knots in DNA can be reinforced considerably by high salt conditions and confinement between plates. Likewise, knots can almost be dissolved completely in a low salt scenario. Comparisons with recent experiments confirm that the coarse-grained model is able to capture and quantitatively predict topological features of DNA and can be used for guiding future experiments on DNA knots.
Submission history
From: Sarah Wettermann [view email][v1] Mon, 14 Nov 2022 13:07:06 GMT (1212kb,D)
[v2] Fri, 23 Dec 2022 13:34:12 GMT (1257kb,D)
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