The length and viscosity dependence of end-to-end collision rates in single-stranded DNA.
The length and viscosity dependence of end-to-end collision rates in single-stranded DNA.
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DOI：
10.1016/j.bpj.2009.04.036
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发表时间：
2009-07
影响因子：
3.4
通讯作者：
T. Uzawa;R. R. Cheng-R.;K. Cash;D. Makarov;K. Plaxco
中科院分区：
文献类型：
--
作者：
T. Uzawa;R. R. Cheng-R.;K. Cash;D. Makarov;K. Plaxco
分子内动力学在生物分子的折叠和功能中起着至关重要的作用，并且越来越多地在许多仿生技术的操作中发挥作用。因此，我们采用实验和模拟来表征从6到26个碱基不等的非结构化单链dna的端到端碰撞动力学。我们发现，由于实验采用的光学报告的大小和灵活性，端到端碰撞动力学在长度尺度<11个碱基时表现出很少的长度依赖性。然而，对于较长的结构，端到端碰撞率与聚合物长度呈幂律关系，指数为−3.49±0.13。这比实验中观察到的非结构化多肽或聚合物缩放参数预测的长度依赖性强得多。然而，模拟表明，较大的指数源于静电效应，在这些高电荷聚合物的相当短的长度尺度上变得重要。最后，我们发现端到端碰撞率也与溶剂粘度呈线性关系，具有实验意义的非零截距（零粘度时的外推率）与链长无关，这一观察结果为许多聚合物系统动力学中观察到的“内摩擦”的起源提供了新的线索。
Intramolecular dynamics play an essential role in the folding and function of biomolecules and, increasingly, in the operation of many biomimetic technologies. Thus motivated we have employed both experiment and simulation to characterize the end-to-end collision dynamics of unstructured, single-stranded DNAs ranging from 6 to 26 bases. We find that, because of the size and flexibility of the optical reporters employed experimentally, end-to-end collision dynamics exhibit little length dependence at length scales <11 bases. For longer constructs, however, the end-to-end collision rate exhibits a power-law relationship to polymer length with an exponent of −3.49 ± 0.13. This represents a significantly stronger length dependence than observed experimentally for unstructured polypeptides or predicted by polymer scaling arguments. Simulations indicate, however, that the larger exponent stems from electrostatic effects that become important over the rather short length scale of these highly charged polymers. Finally, we have found that the end-to-end collision rate also depends linearly on solvent viscosity, with an experimentally significant, nonzero intercept (the extrapolated rate at zero viscosity) that is independent of chain length—an observation that sheds new light on the origins of the "internal friction" observed in the dynamics of many polymer systems.