Energy required to pinch a DNA plectoneme

Barde, Céline; Destainville, Nicolas; Manghi, Manoel

doi:10.1103/physreve.97.032412

Cited by 7 publications

(5 citation statements)

References 45 publications

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“…Single-molecule magnetic tweezers experiments combined with fluorescent labelling of DNA [45] and polymer simulations [46] have then shown that the length of plectonemes in vitro are on the order of 1 kb. Electron microscopy [41] and statistical mechanics of plectonemes [47,48] also revealed a diameter of the plectoneme varying between 30 nm at σ −0.025 and 5 nm at σ −0.1. In addition, due to the entropic contribution of branches, it was shown that plectonemic structures become branched and form trees at large scales [47], in accord with both experiments [41] and numerical simulations [43].…”

Section: B 3d Models : Towards the Large Scalesmentioning

confidence: 98%

DNA supercoiling in bacteria: state of play and challenges from a modeling viewpoint

Junier¹,

Ghobadpour²,

Espéli³

et al. 2023

Preprint

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Section: B 3d Models : Towards the Large Scalesmentioning

confidence: 98%

DNA supercoiling in bacteria: state of play and challenges from a modeling viewpoint

Junier¹,

Ghobadpour²,

Espéli³

et al. 2023

Preprint

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“…Single-molecule magnetic tweezers experiments combined with fluorescent labeling of DNA (van Loenhout et al, 2012 ) and polymer simulations (Lepage et al, 2015 ) have then shown that the length of plectonemes in vitro are on the order of 1 kb. Electron microscopy (Boles et al, 1990 ) and statistical mechanics of plectonemes (Marko and Siggia, 1995 ; Barde et al, 2018 ) also revealed a diameter of the plectoneme varying between ≃30 nm at σ≃−0.025 and ≃5 nm at σ≃−0.1. Finally, due to the entropic contribution of branches, Marko and Siggia further showed that plectonemic structures become branched and form trees at large scales (Marko and Siggia, 1995 ), rationalizing both experiments (Boles et al, 1990 ) and numerical simulations (Vologodskii et al, 1992 ).…”

Section: Structural Predictions From Equilibrium Fiber-like Modelsmentioning

confidence: 99%

DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling

Junier,

Ghobadpour,

Espeli

et al. 2023

Front. Microbiol.

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DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax mechanical stresses that are inevitably produced during DNA replication and gene transcription. Supercoiling affects all scales of the spatio-temporal organization of bacterial DNA, from the base pair to the large scale chromosome conformation. Highlighted in vitro and in vivo in the 1960s and 1970s, respectively, the first physical models were proposed concomitantly in order to predict the deformation properties of the double helix. About fifteen years later, polymer physics models demonstrated on larger scales the plectonemic nature and the tree-like organization of supercoiled DNA. Since then, many works have tried to establish a better understanding of the multiple structuring and physiological properties of bacterial DNA in thermodynamic equilibrium and far from equilibrium. The purpose of this essay is to address upcoming challenges by thoroughly exploring the relevance, predictive capacity, and limitations of current physical models, with a specific focus on structural properties beyond the scale of the double helix. We discuss more particularly the problem of DNA conformations, the interplay between DNA supercoiling with gene transcription and DNA replication, its role on nucleoid formation and, finally, the problem of scaling up models. Our primary objective is to foster increased collaboration between physicists and biologists. To achieve this, we have reduced the respective jargon to a minimum and we provide some explanatory background material for the two communities.

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“…( 5) is coupled to the linking number, which is the sum of twist and writhe [Eqs. (7) and (8), respectively]. In the high-force limit, Eq.…”

Section: E Effects Beyond the Twlc Modelmentioning

confidence: 99%

Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond

et al. 2019

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The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling G between twisting and bending, known to arise from the groove asymmetry of the DNA double helix. Here, the effect of G on the statistical mechanics of long DNA molecules subject to applied forces and torques is investigated. We present a perturbative calculation of the effective torsional stiffness C eff for small twist-bend coupling. We find that the "bare" G is "screened" by thermal fluctuations, in the sense that the low-force, long-molecule effective free energy is that of a model with G = 0, but with long-wavelength bending and twisting rigidities that are shifted by G-dependent amounts. Using results for torsional and bending rigidities for freely-fluctuating DNA, we show how our perturbative results can be extended to a non-perturbative regime. These results are in excellent agreement with numerical calculations for Monte Carlo "triad" and molecular dynamics "oxDNA" models, characterized by different degrees of coarse-graining, validating the perturbative and non-perturbative analyses. While our theory is in generally-good quantitative agreement with experiment, the predicted torsional stiffness does systematically deviate from experimental data, suggesting that there are as-yet-uncharacterized aspects of DNA twisting-stretching mechanics relevant to low-force, long-molecule mechanical response, which are not captured by widely-used coarse-grained models. arXiv:1809.07050v2 [cond-mat.stat-mech]

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Energy required to pinch a DNA plectoneme

Cited by 7 publications

References 45 publications

DNA supercoiling in bacteria: state of play and challenges from a modeling viewpoint

DNA supercoiling in bacteria: state of play and challenges from a modeling viewpoint

DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling

Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond

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