Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom.
School of Physics, Institute for Research in Fundamental Sciences (IPM) , Tehran 19538-33511, Iran.
ACS Nano. 2015 Dec 22;9(12):11993-2003. doi: 10.1021/acsnano.5b04726. Epub 2015 Nov 30.
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.
在应激条件下，双链 DNA 的断裂是生物物理学和纳米技术中的一个关键过程。本文考虑了短 DNA 双链在剪切力作用下的断裂，这个系统最近在设计的力传感器和纳米技术设备中得到了新的重视。我们认为，断裂必须被理解为一个激活过程，在这个过程中，双链状态是亚稳态的，在有限的时间内，链会分离，这个时间取决于双链的长度和施加的力。因此，断裂双链所需的临界剪切力强烈依赖于观察的时间尺度。我们使用简单的 DNA 模型表明，这种方法自然地捕捉到了在给定时间内断裂双链所需的力与双链长度的关系。具体来说，对于最短的双链，这个临界力为零，然后急剧上升，然后在长链极限下趋于平稳。目前的方法基于识别双链中每个额外碱基对的存在在热力学上是不利的，而不是允许亚稳态的存在，这种方法不能预测与时间相关的临界力，也不能自然地将最短双链的临界力为零纳入其中。我们证明了我们的发现对一种新的力传感纳米器件的行为有重要影响，该器件在剪切和拉链两种混合模式下工作。在固定的时间尺度和双链长度下，临界力与受剪切的双链部分的分数呈类正弦函数关系。
