Is hairpin formation in single-stranded polynucleotide diffusion-controlled?
Is hairpin formation in single-stranded polynucleotide diffusion-controlled?
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DOI：
10.1021/jp044838a
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发表时间：
2005-07-07
影响因子：
3.3
通讯作者：
Kuznetsov, SV
中科院分区：
文献类型：
--
作者：
Ansari, A;Kuznetsov, SV
生物聚合物科学中一个有趣的谜题是观察到单链DNA和RNA低聚物在几十微秒的时间尺度上形成发夹结构，比类似长度的无弹性聚合物形成环路的估计时间要慢得多。为了确定发夹动力学是否受扩散控制，研究了溶剂粘度(y)对发夹动力学的影响。粘度是通过添加甘油来改变的，这显著地破坏了发夹的稳定性。先前关于发夹动力学黏度依赖性的研究（Wallace等）。Proc。国家的。学会科学。（美国2000,98,5584），其中测量速率的所有变化都归因于溶剂粘度的变化，报告了弛豫时间（tau(r)）在eta上的明显标度，tau(r)与eta（0.8）相似。在本研究中，我们证明，如果粘度对测量速率的影响没有从稳定性变化的不可避免的影响中解卷积，那么将tau(r)分离为打开（tau(o)）和关闭（tau(c)）时间会产生错误的行为，具有不同的值（和相反的符号）的表观缩放指数，tau(o)类似于eta（-0.4）和tau(c)类似于eta（1.5）。在等稳定条件下，通过改变温度来补偿甘油的不稳定作用，tau(o)和tau(c)的尺度类似于eta 1:1 +/- 0.1。因此，发夹动力学与溶剂粘度紧密耦合，表明多核苷酸链通过溶剂的扩散参与了速率决定步骤。
An intriguing puzzle in biopolymer science is the observation that single-stranded DNA and RNA oligomers form hairpin structures on time scales of tens of microseconds, considerably slower than the estimated time for loop formation for a serniflexible polymer of similar length. To address the origin of the slow kinetics and to determine whether hairpin dynamics are diffusion-controlled, the effect of solvent viscosity (y) on hairpin kinetics was investigated using laser temperature-jump techniques. The viscosity was varied by addition of glycerol, which significantly destabilizes hairpins. A previous study on the viscosity dependence of hairpin dynamics (Wallace et al. Proc. Natl. Acad. Sci. U.S.A. 2000, 98, 5584), in which all the changes in the measured rates were attributed to a change in solvent viscosity, reported an apparent scaling of relaxation times (tau(r)) on eta as tau(r) similar to eta(0.8). In this study, we demonstrate that if the effect of viscosity on the measured rates is not deconvoluted from the inevitable effect of change in stability, then separation of tau(r) into opening (tau(o)) and closing (tau(c)) times yields erroneous behavior, with different values (and opposite signs) of the apparent scaling exponents, tau(o) similar to eta(-0.4) and tau(c) similar to eta(1.5). Under isostability conditions, obtained by varying the temperature to compensate for the destabilizing effect of glycerol, both tau(o) and tau(c) scale as similar to eta 1:1 +/- 0.1. Thus, hairpin dynamics are strongly coupled to solvent viscosity, indicating that diffusion of the polynucleotide chain through the solvent is involved in the rate-determining step.