Department of Physics, University of California, Santa Barbara, CA.
Biophys J. 2013 Dec 3;105(11):2569-76. doi: 10.1016/j.bpj.2013.10.019.
In the absence of base-pairing and tertiary structure, ribonucleic acid (RNA) assumes a random-walk conformation, modulated by the electrostatic self-repulsion of the charged, flexible backbone. This behavior is often modeled as a Kratky-Porod "wormlike chain" (WLC) with a Barrat-Joanny scale-dependent persistence length. In this study we report measurements of the end-to-end extension of poly(U) RNA under 0.1 to 10 pN applied force and observe two distinct elastic-response regimes: a low-force, power-law regime characteristic of a chain of swollen blobs on long length scales and a high-force, salt-valence-dependent regime consistent with ion-stabilized crumpling on short length scales. This short-scale structure is additionally supported by force- and salt-dependent quantification of the RNA ion atmosphere composition, which shows that ions are liberated under stretching; the number of ions liberated increases with increasing bulk salt concentration. Both this result and the observation of two elastic-response regimes directly contradict the WLC model, which predicts a single elastic regime across all forces and, when accounting for scale-dependent persistence length, the opposite trend in ion release with salt concentration. We conclude that RNA is better described as a "snakelike chain," characterized by smooth bending on long length scales and ion-stabilized crumpling on short length scales. In monovalent salt, these two regimes are separated by a characteristic length that scales with the Debye screening length, highlighting the determining importance of electrostatics in RNA conformation.
在没有碱基配对和三级结构的情况下，核糖核酸（RNA）呈现出无规行走构象，受带电、柔性骨架的静电自斥调制。这种行为通常被建模为具有 Barrat-Joanny 标度相关的持久长度的 Kratky-Porod“线状链”（WLC）。在这项研究中，我们报告了在 0.1 到 10 pN 施加力下聚（U）RNA 的末端到末端延伸的测量结果，并观察到两个不同的弹性响应区：低力、幂律区，特征是长尺度上的肿胀小球链，以及高力、盐价依赖性区，与短尺度上的离子稳定褶皱一致。这种短尺度结构还通过对 RNA 离子气氛组成的力和盐依赖性定量得到了支持，这表明离子在拉伸下被释放；随着体相盐浓度的增加，释放的离子数量增加。这一结果和两个弹性响应区的观察直接与 WLC 模型相矛盾，该模型预测在所有力下都存在单一的弹性区，并且在考虑到标度相关的持久长度时，离子释放与盐浓度呈相反趋势。我们得出结论，RNA 更适合描述为“蛇形链”，其特征是在长尺度上平滑弯曲，在短尺度上离子稳定褶皱。在单价盐中，这两个区被一个与 Debye 屏蔽长度标度的特征长度隔开，突出了静电在 RNA 构象中的决定性重要性。
