The rate of intramolecular loop formation in DNA and polypeptides: the absence of the diffusion-controlled limit and fractional power-law viscosity dependence.
The rate of intramolecular loop formation in DNA and polypeptides: the absence of the diffusion-controlled limit and fractional power-law viscosity dependence.
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DOI：
10.1021/jp902291n
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发表时间：
2009-10-22
期刊：
影响因子：
--
通讯作者：
Makarov DE
中科院分区：
文献类型：
--
作者：
Cheng RR;Uzawa T;Plaxco KW;Makarov DE
确定高分子链的端对端碰撞速率的问题已经吸引了理论家和实验学家三十多年的注意力。解决这个问题的典型理论方法集中在碰撞被定义为使链端在特定捕获距离内的任何瞬时波动的情况下。在本文中，我们研究了更多的实验相关的情况下，端到端的碰撞动力学探测通过测量的激发态寿命的荧光团（或其他发光团）连接到一个链端和淬灭基团连接到另一端。在这种情况下，“接触”不是由链端接近某个尖锐的截止来定义的，而是通常由指数距离依赖性过程来定义的。以前的理论模型预测，如果淬火是足够快的，扩散控制的限制达到，这样的测量报告的探针独立的，固有的端到端的碰撞率。相比之下，我们的理论考虑，模拟，并在单链DNA分子中的环闭合率的实验测量的分析都表明，没有这样的限制存在，并且测得的有效碰撞率有一个非平凡的，分数幂律依赖于荧光团的固有猝灭率和溶剂粘度。我们提出了一个简单的缩放公式描述的有效闭环速率和它的依赖性的粘度，链长，和性质的探针。以前的理论结果是这个更一般的公式的限制情况。
The problem of determining the rate of end-to-end collisions for polymer chains has attracted the attention of theorists and experimentalists for more than three decades. The typical theoretical approach to this problem has focused on the case where a collision is defined as any instantaneous fluctuation that brings the chain ends to within a specific capture distance. In this paper, we study the more experimentally relevant case, where the end-to-end collision dynamics are probed by measuring the excited state lifetime of a fluorophore (or other lumiphore) attached to one chain end and quenched by a quencher group attached to the other end. Under this regime, a “contact” is defined not by the chain ends approach to within some sharp cutoff but, instead, typically by an exponentially distance-dependent process. Previous theoretical models predict that, if quenching is sufficiently rapid, a diffusion-controlled limit is attained, where such measurements report on the probe-independent, intrinsic end-to-end collision rate. In contrast, our theoretical considerations, simulations, and an analysis of experimental measurements of loop closure rates in single-stranded DNA molecules all indicate that no such limit exists, and that the measured effective collision rate has a nontrivial, fractional power-law dependence on both the intrinsic quenching rate of the fluorophore and the solvent viscosity. We propose a simple scaling formula describing the effective loop closure rate and its dependence on the viscosity, chain length, and properties of the probes. Previous theoretical results are limiting cases of this more general formula.
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