Kundu Prasanta, Saha Soma, Gangopadhyay Gautam
S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India.
Department of Chemistry, Presidency University, 86/1 College Street, Kolkata 700073, India.
J Phys Chem B. 2020 Jul 30;124(30):6575-6584. doi: 10.1021/acs.jpcb.0c05122. Epub 2020 Jul 16.
Escape experiments probed the dynamics of DNA hairpins inside a membrane-embedded α-hemolysin channel, which revealed the orientation and voltage-dependent nature of the DNA-pore interactions. The mean escape times measured at different assisting voltages were strongly influenced by these interactions. Clearly, an escape process from the nanopore was stochastic in nature that occurred in milliseconds. In this paper, we present a new methodology for describing the experimental observations based on the stochastic kinetic approach of discrete-state and continuous-time formulations. Our model considers that a hairpin attains different states inside and out of the pore, and we derived the expression for the escape time distribution from which survival probability of the hairpin that still exists inside the nanopore is determined. On the other hand, the first moment of the above distribution readily yields the mean escape time. Importantly, we show that the recovery of the experimental results was possible taking into account the slow structural fluctuations of the combined DNA-pore system. Additional investigation tested the profound influence of conformational dynamics by considering a pure kinetic scheme, which satisfied the measured data only partially. Therefore, the single stochastic framework suggested here provides a powerful tool that leads to a significant improvement in the theoretical analysis of the experimental results over a range of applied voltages by removing the inadequacy of the original attempt constructed following a number of formulations in the absence of intrinsic fluctuations.
逃逸实验探究了嵌入膜中的α-溶血素通道内DNA发夹的动力学，揭示了DNA与孔相互作用的取向和电压依赖性本质。在不同辅助电压下测得的平均逃逸时间受到这些相互作用的强烈影响。显然，从纳米孔的逃逸过程本质上是随机的，发生在毫秒级。在本文中，我们基于离散状态和连续时间公式的随机动力学方法，提出了一种描述实验观察结果的新方法。我们的模型认为发夹在孔内外达到不同状态，并推导了逃逸时间分布的表达式，由此确定了仍存在于纳米孔内的发夹的存活概率。另一方面，上述分布的一阶矩很容易得出平均逃逸时间。重要的是，我们表明考虑到DNA-孔组合系统的缓慢结构波动，恢复实验结果是可能的。通过考虑一个纯动力学方案进行的额外研究测试了构象动力学的深远影响，该方案仅部分满足测量数据。因此，这里提出的单一随机框架提供了一个强大的工具，通过消除在没有内在波动的情况下按照多种公式构建的原始尝试的不足，在一系列施加电压范围内显著改进了实验结果的理论分析。
