Plectoneme dynamics and statistics in braided polymers

Forte, Giada; Caraglio, Michele; Marenduzzo, Davide; Orlandini, Enzo

doi:10.1103/physreve.99.052503

Cited by 12 publications

(20 citation statements)

References 26 publications

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“…As for the obtained value of diffusivity of supercoiling, D σ = 1.6, agrees well with the value obtained by the study of plectoneme dynamics of braided polymers like DNA by Forte et al [49]. In their study, the authors observed that the dynamics of twist is faster than that of writhe, while the obtained decoupled diffusivities were D Tw = 2.0 and D Wr = 0.1, giving the value of diffusivity of supercoiling as a weighted average with contributions of each based on whether the system accommodates a stable plectonemic or straight conformation.…”

Section: Mathematic Model Of Transcriptionally Driven Loop Extrusionsupporting

confidence: 91%

Entropic Competition between Supercoiled and Torsionally Relaxed Chromatin Fibers Drives Loop Extrusion through Pseudo-Topologically Bound Cohesin

Rusková

Račko

2021

Biology

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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.

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Section: Mathematic Model Of Transcriptionally Driven Loop Extrusionsupporting

confidence: 91%

Entropic Competition between Supercoiled and Torsionally Relaxed Chromatin Fibers Drives Loop Extrusion through Pseudo-Topologically Bound Cohesin

Rusková

Račko

2021

Biology

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“…This system is known to display a buckling transition at a critical catenation number Ca* which depends on the stretching force f, i.e. Ca* = Ca*( f ) [26][27][28][29][30]. For Ca < Ca*( f ), the braid is straight whereas for Ca > Ca*( f ) the braid buckles and forms plectonemes that resemble those shown by single dsDNA molecules in MT assays [31][32][33].…”

Section: Introductionmentioning

confidence: 99%

Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids

Forte

Michieletto

Marenduzzo

et al. 2021

J. R. Soc. Interface.

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We theoretically study the integration of short viral DNA in a DNA braid made up by two entwined double-stranded DNA molecules. We show that the statistics of single integration events substantially differ in the straight and buckled, or plectonemic, phase of the braid and are more likely in the latter. We further discover that integration is most likely close to plectoneme tips, where the larger bending energy helps overcome the associated energy barrier and that successive integration events are spatio-temporally correlated, suggesting a potential mechanistic explanation of clustered integration sites in host genomes. The braid geometry we consider provides a novel experimental set-up to quantify integration in a supercoiled substrate in vitro , and to better understand the role of double-stranded DNA topology during this process.

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“…Our results show that polar writhe is not only applicable to the analysis of open curves such as those formed by extended DNA structures but that it can be decomposed into local and nonlocal contributions that can provide additional information about DNA topology that cannot be obtained from the Călugăreanu formalism. In particular, we demonstrate how the non-local component of the polar writhe can be used as a potential indicator of plectoneme formation in both linear and circular DNA structures which we believe will be of particular value to the host of studies performed on effects of plectoneme formation in DNA and braided polymers 54,55 . To aid in the adoption of polar writhe, we have developed a software package, WASP, that can be used to analyze molecular dynamics simulations of DNA.…”

Section: Discussionmentioning

confidence: 84%

WASP: a software package for correctly characterizing the topological development of ribbon structures

Sierzega

Wereszczynski

Prior

2021

Sci Rep

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We introduce the Writhe Application Software Package (WASP) which can be used to characterisze the topology of ribbon structures, the underlying mathematical model of DNA, Biopolymers, superfluid vorticies, elastic ropes and magnetic flux ropes. This characterization is achieved by the general twist–writhe decomposition of both open and closed ribbons, in particular through a quantity termed the polar writhe. We demonstrate how this decomposition is far more natural and straightforward than artificial closure methods commonly utilized in DNA modelling. In particular, we demonstrate how the decomposition of the polar writhe into local and non-local components distinctly characterizes the local helical structure and knotting/linking of the ribbon. This decomposition provides additional information not given by alternative approaches. As example applications, the WASP routines are used to characterise the evolving topology (writhe) of DNA minicircle and open ended plectoneme formation magnetic/optical tweezer simulations, and it is shown that the decomponsition into local and non-local components is particularly important for the detection of plectonemes. Finally it is demonstrated that a number of well known alternative writhe expressions are actually simplifications of the polar writhe measure.

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Plectoneme dynamics and statistics in braided polymers

Cited by 12 publications

References 26 publications

Entropic Competition between Supercoiled and Torsionally Relaxed Chromatin Fibers Drives Loop Extrusion through Pseudo-Topologically Bound Cohesin

Entropic Competition between Supercoiled and Torsionally Relaxed Chromatin Fibers Drives Loop Extrusion through Pseudo-Topologically Bound Cohesin

Investigating site-selection mechanisms of retroviral integration in supercoiled DNA braids

WASP: a software package for correctly characterizing the topological development of ribbon structures

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