Ansari Anjum, Kuznetsov Serguei V
Department of Physics and Department of Bioengineering, University of Illinois at Chicago, 845 West Taylor Street, Chicago, Illinois 60607, USA.
J Phys Chem B. 2005 Jul 7;109(26):12982-9. doi: 10.1021/jp044838a.
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 semiflexible 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 (eta) 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, 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) approximately 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) approximately eta(-0.4) and tau(c) approximately 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 approximately 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.
生物聚合物科学中一个有趣的谜题是,观察到单链DNA和RNA低聚物在数十微秒的时间尺度上形成发夹结构,这比类似长度的半柔性聚合物形成环的估计时间要慢得多。为了解决动力学缓慢的起源问题,并确定发夹动力学是否受扩散控制,使用激光温度跳跃技术研究了溶剂粘度(η)对发夹动力学的影响。通过添加甘油来改变粘度,甘油会显著使发夹不稳定。先前一项关于发夹动力学粘度依赖性的研究,将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(τr)与η的明显标度关系为τr约为η(0.8)。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必然影响中解卷积出来,那么将τr分为打开时间(τo)和关闭时间(τc)会产生错误的行为,表观标度指数有不同的值(且符号相反),τo约为η(-0.4),τc约为η(-)。在通过改变温度以补偿甘油的去稳定作用而获得的等稳定性条件下,τo和τc都按约为η(1.1±0.1)标度。因此,发夹动力学与溶剂粘度紧密相关,这表明多核苷酸链在溶剂中的扩散参与了速率决定步骤。