On the rupture of DNA molecule

Mishra, Rakesh; Modi, Tushar; Giri, Debasis; Kumar, Sanjay

doi:10.1063/1.4919646

Cited by 8 publications

(5 citation statements)

References 34 publications

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“…The situation is drastically different in biological applications where, for instance, cell adhesion is characterized by low binding energies of the order of k B T , which is ∼ 4.1 pN nm at physiological temperatures T ∼ 300 K. Such weak bonding can be disrupted by thermal activation leading to finite lifetimes of the bonds [12][13][14]. As a result, the temperature can be an important factor controlling the debonding processes; in particular, it plays a crucial role in the zipping-unzipping phenomena involved in the functioning of biological macromolecules [15][16][17][18].…”

Section: Introductionmentioning

confidence: 99%

Equilibrium unzipping at finite temperature

Rocha

Truskinovsky

2018

Arch Appl Mech

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We study thermally activated unzipping, which is modeled as a debonding process. The system is modeled as a parallel bundle of elastically interacting breakable units loaded through a series spring. Using equilibrium statistical mechanics, we compute the reversible response of this mechanical system under quasi-static driving. Depending on the stiffness of the series spring, the system exhibits either ductile behavior, characterized by noncooperative debonding, or brittle behavior, with a highly correlated detachment of the whole bundle. We show that the ductile to brittle transition is of the second order and that it can also be controlled by temperature.

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Section: Introductionmentioning

confidence: 99%

Equilibrium unzipping at finite temperature

Rocha

Truskinovsky

2018

Arch Appl Mech

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“…15,16,24 Despite this history, the physical principles highlighted by the toy model have not been widely applied to understand the dependence of the critical shearing force on duplex length. 25,29,30,37,38,47 The alternative reasoning originated from de Gennes, who modelled DNA as a ladder with springs connecting neighbors within a strand and bases paired by interstrand hydrogen bonding. 29 He calculated the mechanical equilibrium of this system under applied shearing stress, and posited that an individual base-pair spring with extension above a certain critical value would rupture.…”

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confidence: 99%

“…Broadly similar reasoning to that underlying the toy model has been applied to the unzipping of DNA (in which two strands are pulled apart from the same end of the duplex; see Figure b), although the approach in ref cannot directly be used to understand the more complex geometry of shearing. Experiments in which force is applied dynamically have also been analyzed in terms of models of activated processes. ,, Despite this history, the physical principles highlighted by the toy model have not been widely applied to understand the dependence of the critical shearing force on duplex length. ,,,,, The alternative reasoning originated from de Gennes, who modeled DNA as a ladder with springs connecting neighbors within a strand and bases paired by interstrand hydrogen bonding . He calculated the mechanical equilibrium of this system under applied shearing stress and posited that an individual base-pair spring with extension above a certain critical value would rupture.…”

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confidence: 99%

Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors

et al. 2015

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The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article, we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed force sensors and nanotechnological devices. We argue that rupture must be understood as an activated process, where the duplex state is metastable and the strands will separate in a finite time that depends on the duplex length and the force applied. Thus, the critical shearing force required to rupture a duplex depends strongly on the time scale of observation. We use simple models of DNA to show that this approach naturally captures the observed dependence of the force required to rupture a duplex within a given time on duplex length. In particular, this critical force is zero for the shortest duplexes, before rising sharply and then plateauing in the long length limit. The prevailing approach, based on identifying when the presence of each additional base pair within the duplex is thermodynamically unfavorable rather than allowing for metastability, does not predict a time-scale-dependent critical force and does not naturally incorporate a critical force of zero for the shortest duplexes. We demonstrate that our findings have important consequences for the behavior of a new force-sensing nanodevice, which operates in a mixed mode that interpolates between shearing and unzipping. At a fixed time scale and duplex length, the critical force exhibits a sigmoidal dependence on the fraction of the duplex that is subject to shearing.

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“…The structure of the overstretched state of the DNA is not yet fully resolved and is under intense debate [8,9,14,[32][33][34][35][38][39][40] over the last two decades. Thus it is still an open question whether the overstretching transition leads to FIM or gives rise to S-DNA.…”

Section: Introductionmentioning

confidence: 99%

Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA

Garai

Mogurampelly

Bag

et al. 2017

The Journal of Chemical Physics

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We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics simulations reveal a clear formation of S-DNA when the B-DNA is stretched along the 3 ′ directions of the opposite strands (OS3) and is characterized by the changes in the number of H-bonds, entropy and free energy. Stretching along 5 ′ directions of the opposite strands (OS5) leads to force induced melting form of the DNA.Interestingly, stretching along the opposite ends of the same strand (SS) leads to a coexistence of both the S-and melted M-DNA structures. We also do the structural characterization of the S-DNA by calculating various helical parameters. We find that S-DNA has a twist of ∼ 10 degrees which corresponds to helical repeat length of ∼ 36 base pairs in close agreement with the previous experimental results. Moreover, we find that the free energy barrier between the canonical and overstretched states of DNA is higher for the same termini (SE) pulling protocol in comparison to all other protocols considered in this work. Overall, our observations not only reconcile with the available experimental results qualitatively but also enhance the understanding of different overstretched DNA structures.

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On the rupture of DNA molecule

Cited by 8 publications

References 34 publications

Equilibrium unzipping at finite temperature

Equilibrium unzipping at finite temperature

Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors

Overstretching of B-DNA with various pulling protocols: Appearance of structural polymorphism and S-DNA

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