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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes
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Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes

机译：RNA发夹的依赖于力的跳跃率可以通过对折叠景观的精确测量来估算

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摘要

The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated by using single-molecule force-clamp experiments by attaching semiflexible polymers to the ends of hairpins, have been used to infer their folding landscapes. Using simulations and theory, we study the effect of the dynamics of the attached handles on the handle-free RNA free-energy profile F°_(eq)(z_m), where z_m is the molecular extension of the hairpin. Accurate measurements ofrnF°_(eq)(z_m) requires stiff polymers with small L/I_p, where L is the contour length of the handle, and I_p is the persistence length. Paradoxically, reliable estimates of the hopping rates can only be made by using flexible handles. Nevertheless, we show that the equilibrium free-energy profile F°_(eq)(z_m) at an external tension f_m, the force (f) at which the folded and unfolded states are equally populated, in conjunction with Kramers' theory, can provide accurate estimates of the force-dependent hopping rates in the absence of handles at arbitrary values of f. Our theoretical framework shows that z_m is a good reaction coordinate for nucleic acid hairpins under tension.
机译：核酸发夹的序列依赖性折叠态势反映了生物分子折叠的许多复杂性。通过使用单分子力钳实验通过将半柔性聚合物附着到发夹的末端而生成的折叠轨迹已用于推断其折叠情况。使用模拟和理论，我们研究了附加的手柄的动力学对无手柄RNA自由能图F°_（eq）（z_m）的影响，其中z_m是发夹的分子延伸。 rnF°_（eq）（z_m）的准确测量需要具有较小L / I_p的硬质聚合物，其中L是手柄的轮廓长度，I_p是持久长度。矛盾的是，只能通过使用灵活的句柄来可靠地估计跳跃率。然而，我们表明，在外部张力f_m下，结合Kramers理论，在相等的折叠和展开状态下的力（f）可以达到平衡自由能曲线F°_（eq）（z_m）。在不存在任何f值的句柄的情况下，提供与力有关的跳跃率的准确估计。我们的理论框架表明，z_m是处于张力下的核酸发夹的良好反应坐标。

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