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Authors = Dušan Račko ORCID = 0000-0002-9203-9652

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18 pages, 2345 KiB  
Article
Knot Formation on DNA Pushed Inside Chiral Nanochannels
by Renáta Rusková and Dušan Račko
Polymers 2023, 15(20), 4185; https://doi.org/10.3390/polym15204185 - 22 Oct 2023
Cited by 5 | Viewed by 9565
Abstract
We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We [...] Read more.
We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also compared the regime of pushing a polymer inside the infinite channel to the case of polymer compression in finite channels of knot factories investigated in earlier works. We observed that the compression in the open channels affects the polymer metrics to different extents in chiral and achiral channels. We also observed that the chiral channels give rise to the formation of equichiral knots with the same handedness as the handedness of the chiral channels. Full article
(This article belongs to the Special Issue Polymer Physics: From Theory to Experimental Applications)
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22 pages, 4531 KiB  
Article
Knot Factories with Helical Geometry Enhance Knotting and Induce Handedness to Knots
by Renáta Rusková and Dušan Račko
Polymers 2022, 14(19), 4201; https://doi.org/10.3390/polym14194201 - 7 Oct 2022
Cited by 2 | Viewed by 84722
Abstract
We performed molecular dynamics simulations of DNA polymer chains confined in helical nano-channels under compression in order to explore the potential of knot-factories with helical geometry to produce knots with a preferred handedness. In our simulations, we explore mutual effect of the confinement [...] Read more.
We performed molecular dynamics simulations of DNA polymer chains confined in helical nano-channels under compression in order to explore the potential of knot-factories with helical geometry to produce knots with a preferred handedness. In our simulations, we explore mutual effect of the confinement strength and compressive forces in a range covering weak, intermediate and strong confinement together with weak and strong compressive forces. The results find that while the common metrics of polymer chain in cylindrical and helical channels are very similar, the DNA in helical channels exhibits greatly different topology in terms of chain knottedness, writhe and handedness of knots. The results show that knots with a preferred chirality in terms of average writhe can be produced by using channels with a chosen handedness. Full article
(This article belongs to the Special Issue Molecular Simulation and Modeling of Polymers)
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25 pages, 3882 KiB  
Article
Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures
by Renáta Rusková and Dušan Račko
Polymers 2021, 13(21), 3726; https://doi.org/10.3390/polym13213726 - 28 Oct 2021
Cited by 5 | Viewed by 27495
Abstract
By means of coarse-grained molecular dynamics simulations, we explore chiral sensitivity of confining spaces modelled as helical channels to chiral superstructures represented by polymer knots. The simulations show that helical channels exhibit stereosensitivity to chiral knots localized on linear chains by effect of [...] Read more.
By means of coarse-grained molecular dynamics simulations, we explore chiral sensitivity of confining spaces modelled as helical channels to chiral superstructures represented by polymer knots. The simulations show that helical channels exhibit stereosensitivity to chiral knots localized on linear chains by effect of external pulling force and also to knots embedded on circular chains. The magnitude of the stereoselective effect is stronger for torus knots, the effect is weaker in the case of twist knots, and amphichiral knots do exhibit no chiral effects. The magnitude of the effect can be tuned by the so-far investigated radius of the helix, the pitch of the helix and the strength of the pulling force. The model is aimed to simulate and address a range of practical situations that may occur in experimental settings such as designing of nanotechnological devices for the detection of topological state of molecules, preparation of new gels with tailor made stereoselective properties, or diffusion of knotted DNA in biological conditions. Full article
(This article belongs to the Special Issue Molecular Simulation and Modeling of Polymers)
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15 pages, 2084 KiB  
Article
Entropic Competition between Supercoiled and Torsionally Relaxed Chromatin Fibers Drives Loop Extrusion through Pseudo-Topologically Bound Cohesin
by Renáta Rusková and Dušan Račko
Biology 2021, 10(2), 130; https://doi.org/10.3390/biology10020130 - 7 Feb 2021
Cited by 9 | Viewed by 60853
Abstract
We propose a model for cohesin-mediated loop extrusion, where the loop extrusion is driven entropically by the energy difference between supercoiled and torsionally relaxed chromatin fibers. Different levels of negative supercoiling are controlled by varying imposed friction between the cohesin ring and the [...] Read more.
We propose a model for cohesin-mediated loop extrusion, where the loop extrusion is driven entropically by the energy difference between supercoiled and torsionally relaxed chromatin fibers. Different levels of negative supercoiling are controlled by varying imposed friction between the cohesin ring and the chromatin fiber. The speed of generation of negative supercoiling by RNA polymerase associated with TOP1 is kept constant and corresponds to 10 rotations per second. The model was tested by coarse-grained molecular simulations for a wide range of frictions between 2 to 200 folds of that of generic fiber and the surrounding medium. The higher friction allowed for the accumulation of higher levels of supercoiling, while the resulting extrusion rate also increased. The obtained extrusion rates for the given range of investigated frictions were between 1 and 10 kbps, but also a saturation of the rate at high frictions was observed. The calculated contact maps indicate a qualitative improvement obtained at lower levels of supercoiling. The fits of mathematical equations qualitatively reproduce the loop sizes and levels of supercoiling obtained from simulations and support the proposed mechanism of entropically driven extrusion. The cohesin ring is bound on the fibers pseudo-topologically, and the model suggests that the topological binding is not necessary. Full article
(This article belongs to the Special Issue Chromatin Dynamics)
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