Shear unzipping of double-stranded DNA

Prakash, Shiv; Singh, Yashwant

doi:10.1103/physreve.84.031905

Cited by 11 publications

(20 citation statements)

References 34 publications

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“…Previous work has contended that the shape of f c (N ) arises because a shorter duplex is immediately unstable to rupture (rather than metastable with a short enough life time) at a lower force than longer duplexes. 25,29,30,37,38 We see evidence that shorter duplexes are indeed unstable at lower forces in our data for oxDNA, but we argue that this is not the primary factor in determining the shape of f c (N ). Conceptually, it is clear that any theory that describes whether a molecular system undergoes change on a time scale of seconds or more should allow for metastability.…”

Section: Discussionmentioning

confidence: 49%

“…[15][16][17][18][19][20][21][22][23][24][25][26][27] Simultaneously, theoretical models have been developed to predict and explain the experimental results. 15,16,19,[24][25][26][28][29][30][31][32][33][34][35][36][37][38] In this article we study the physics underlying shearing of short DNA duplexes, illustrated in Fig. 1 (a).…”

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confidence: 99%

“…Such a setup has been explored experimentally 9,[15][16][17][22][23][24][25] and theoretically. 15,16,24,25,29,30,34,37,38 In early experiments, 15-17,22-24 loads were increased dynamically; more recently, Hatch et al were able to use a constant force. 25 Clearly, for any non-zero constant force, the stable state involves widely separated strands:…”

mentioning

confidence: 99%

“…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%

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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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Section: Discussionmentioning

confidence: 49%

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confidence: 99%

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confidence: 99%

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

et al. 2015

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“…Equation 1shows that the shear force increases linearly with l (for small lengths), and saturates at higher values of l, which is consistent with the experiment [10]. Different models similar to the ladder model have been studied and explored the different aspects of DNA rupture [17][18][19][20].…”

Section: Introductionsupporting

confidence: 60%

On the rupture of DNA molecule

Mishra

Modi

Giri

et al. 2015

The Journal of Chemical Physics

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Using Langevin dynamics simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of individual segments of diblock copolymer are considered to be different. We showed that the magnitude of the rupture force depends on whether the force is applied at 3' - 3' - ends or 5' - 5' - ends. Distributions of extension in hydrogen bonds and covalent bonds along the chain show the striking differences. Motivated by recent experiments, we have also calculated the variation of rupture force for different chain lengths. Results obtained from simulations have been validated with the analytical calculation based on the ladder model of DNA.

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Unraveling the Dual-Stretch-Mode Impact on Tension Gauge Tethers’ Mechanical Stability

Liu,

Yan

2024

J. Am. Chem. Soc.

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Tension gauge tethers (TGTs), short DNA segments serving as extracellular tension sensors, are instrumental in assessing the tension dynamics in mechanotransduction. These TGTs feature an initial shear-stretch region and an unzip-stretch region. Despite their utility, no theoretical model has been available to estimate their tension-dependent lifetimes [τ(f)], restricting insights from cellular mechanotransduction experiments. We have now formulated a concise expression for τ(f) of TGTs, accommodating contributions from both stretch regions. Our model uncovers a tension-dependent energy barrier shift occurring when tension surpasses a switching force of approximately 13 pN for the recently developed TGTs, greatly influencing τ(f) profiles. Experimental data from several TGTs validated our model. The calibrated expression can predict τ(f) of TGTs at 37 °C based on their sequences with minor fold changes, supporting future applications of TGTs.

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Shear unzipping of double-stranded DNA

Cited by 11 publications

References 34 publications

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

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

On the rupture of DNA molecule

Unraveling the Dual-Stretch-Mode Impact on Tension Gauge Tethers’ Mechanical Stability

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