Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments
Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments
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DOI：
10.1529/biophysj.106.094243
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发表时间：
2007-05-01
影响因子：
3.4
通讯作者：
Ritort, F.
中科院分区：
文献类型：
--
作者：
Manosas, M.;Wen, J. -D.;Ritort, F.
通过施加机械力，可以一次展开/重新折叠一个RNA分子。在很小的作用力范围内，RNA分子可以从力相关的运动速率在折叠和未折叠状态之间跳跃。在这里，我们引入一个介观模型来分析光钳装置中RNA发夹的跳跃动力学。该模型包括实验装置的不同元素(珠子、手柄和RNA序列)和仪器的局限性(力反馈机制的时滞和数据采集的有限带宽)。研究了仪器对测量跳频的影响。该模型的计算结果与文中报道的实验结果吻合较好。理论和实验的比较使我们能够单独推断RNA发夹的固有分子速率的值，并寻找进行测量的最佳实验条件。我们的结论是，允许检测折叠/展开信号的最长手柄和最软的陷阱(手柄；5-10 kBP和陷阱；0.03pN/nm)代表了获得本征分子速率的最佳条件。这里介绍的方法和原理可以应用于其他实验装置和其他分子。
By exerting mechanical force, it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hairpins in an optical tweezers setup. The model includes different elements of the experimental setup (beads, handles, and RNA sequence) and limitations of the instrument (time lag of the force-feedback mechanism and finite bandwidth of data acquisition). We investigated the influence of the instrument on the measured hopping rates. Results from the model are in good agreement with the experiments reported in the companion article. The comparison between theory and experiments allowed us to infer the values of the intrinsic molecular rates of the RNA hairpin alone and to search for the optimal experimental conditions to do the measurements. We conclude that the longest handles and softest traps that allow detection of the folding/unfolding signal (handles; 5-10 Kbp and traps; 0.03 pN/nm) represent the best conditions to obtain the intrinsic molecular rates. The methodology and rationale presented here can be applied to other experimental setups and other molecules.