Insights into the Discrepancy between Single Molecule Experiments
Insights into the Discrepancy between Single Molecule Experiments
复制标题
洞察单分子实验之间的差异
DOI：
10.1088/0253-6102/71/6/753
复制
发表时间：
2019
期刊：
影响因子：
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通讯作者：
Yanhui Liu
中科院分区：
文献类型：
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作者：
Qian Zhou;Min Zhang;Yangtao Fan;Yukang Wang;Lin Bao;Guangju Zhao;Hu Chen;Yanhui Liu
作为纳米尺度上双链DNA(DsDNA)的力学性质之一，急剧弯曲对于生物功能和加工是必不可少的。带有光学读数的力传感器被设计用来测量由dsDNA和单链DNA(SsDNA)组成的短而紧张的环中的力。最近的FRET单分子实验都是基于相同的力传感器设计进行的，但得到了完全相反的结果。在目前的工作中，蒙特卡罗模拟在三种情况下进行，以澄清两个实验之间的差异。利用单链DNA作用力做功大于最近邻(NN)堆积相互作用能的判据来识别双链DNA与单链DNA交界处分叉的产生。当传感器中dsDNA的轮廓长度大于其临界长度时，在dsDNA和ssDNA的交界处开始产生叉子，即使dsDNA中有一个扭结。在三种情况下，模拟得到的力与实验得到的力是一致的，包括超大的力，并且可以分为两种不同的状态，即叉态和扭结状态。在NN堆积相互作用能和激发能相空间构建的相图表明，在叉态和扭态的相空间中，叉态和扭态之间的转变很难识别，但在叉态和扭态数目适中的相空间中，这种转变是可以检测到的。
Sharp bending as one of the mechanical properties of double-stranded DNA (dsDNA) on the nanoscale is essential for biological functions and processes. Force sensors with optical readout have been designed to measure the forces inside short, strained loops composed of both dsDNA and single-stranded DNA (ssDNA). Recent FRET single-molecule experiments were carried out based on the same force sensor design, but provided totally contrary results. In the current work, Monte Carlo simulations were performed under three conditions to clarify the discrepancy between the two experiments. The criterion that the work done by the force exerted on dsDNA by ssDNA should be larger than the nearest-neighbor (NN) stacking interaction energy is used to identify the generation of the fork at the junction of dsDNA and ssDNA. When the contour length of dsDNA in the sensor is larger than its critical length, the fork begins to generate at the junction of dsDNA and ssDNA, even with a kink in dsDNA. The forces inferred from simulations under three conditions are consistent with the ones inferred from experiments, including extra large force and can be grouped into two different states, namely, fork states and kink states. The phase diagrams constructed in the phase space of the NN stacking interaction energy and excited energy indicate that the transition between the fork state and kink state is difficult to identify in the phase space with an ultra small or large number of forks, but it can be detected in the phase space with a medium number of forks and kinks.
DOI：
10.1109/worlds450073.2020.9210346
发表时间：
2019-11
期刊：
2020 Fourth World Conference on Smart Trends in Systems, Security and Sustainability (WorldS4)
影响因子：
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作者：
Philip D. Plowright
通讯作者：
Philip D. Plowright