Lehrstuhl für Angewandte Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, Munich, Germany.
Biophys J. 2009 Dec 16;97(12):3158-67. doi: 10.1016/j.bpj.2009.09.040.
Short double-stranded DNA is used in a variety of nanotechnological applications, and for many of them, it is important to know for which forces and which force loading rates the DNA duplex remains stable. In this work, we develop a theoretical model that describes the force-dependent dissociation rate for DNA duplexes tens of basepairs long under tension along their axes ("shear geometry"). Explicitly, we set up a three-state equilibrium model and apply the canonical transition state theory to calculate the kinetic rates for strand unpairing and the rupture-force distribution as a function of the separation velocity of the end-to-end distance. Theory is in excellent agreement with actual single-molecule force spectroscopy results and even allows for the prediction of the rupture-force distribution for a given DNA duplex sequence and separation velocity. We further show that for describing double-stranded DNA separation kinetics, our model is a significant refinement of the conventionally used Bell-Evans model.
短的双链 DNA 被广泛应用于各种纳米技术中，对于许多应用来说，了解双链 DNA 在哪些力和哪些力加载速率下保持稳定是很重要的。在这项工作中，我们开发了一个理论模型，该模型描述了在张力下沿着其轴（“剪切几何”）数十个碱基对长的 DNA 双链体的力依赖性解离率。具体来说，我们建立了一个三态平衡模型，并应用正则过渡态理论来计算链解旋的动力学速率以及作为末端到末端距离分离速度的函数的断裂力分布。理论与实际的单分子力谱结果非常吻合，甚至可以预测给定的 DNA 双链体序列和分离速度的断裂力分布。我们进一步表明，对于描述双链 DNA 分离动力学，我们的模型是传统使用的 Bell-Evans 模型的重要改进。
