The ability to accurately predict RNA hairpin structure and stability for different loop sequences and salt conditions is important for understanding, modeling, and designing larger RNA folds. However, traditional RNA secondary structure models cannot treat loop-sequence and ionic effects on RNA hairpin folding. Here, we describe a general, three-dimensional (3D) conformation-based computational method for modeling salt concentration-dependent conformational distributions and the detailed 3D structures for a set of three RNA hairpins that contain a variable, 15-nucleotide loop sequence. For a given RNA sequence, the new, to our knowledge, method integrates a Vfold2D two-dimensional structure folding model with IsRNA coarse-grained molecular dynamics 3D folding simulations and Monte Carlo tightly bound ion estimations of ion-mediated electrostatic interactions. The model predicts free-energy landscapes for the different RNA hairpin-forming sequences with variable salt conditions. The theoretically predicted results agree with the experimental fluorescence measurements, validating the strategy. Furthermore, the theoretical model goes beyond the experimental results by enabling in-depth 3D structural analysis, revealing energetic mechanisms for the sequence- and salt-dependent folding stability. Although the computational framework presented here is developed for RNA hairpin systems, the general method may be applied to investigate other RNA systems, such as multiway junctions or pseudoknots in mixed metal ion solutions.

中文翻译：

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模拟环组成和离子浓度对 RNA 发夹折叠稳定性的影响


准确预测不同环序列和盐条件下的 RNA 发夹结构和稳定性的能力对于理解、建模和设计更大的 RNA 折叠非常重要。然而，传统的RNA二级结构模型无法处理环序列和离子对RNA发夹折叠的影响。在这里，我们描述了一种基于三维 (3D) 构象的通用计算方法，用于模拟盐浓度依赖性构象分布，以及一组包含可变 15 核苷酸环序列的三个 RNA 发夹的详细 3D 结构。对于给定的 RNA 序列，据我们所知，新方法将 Vfold2D 二维结构折叠模型与 IsRNA 粗粒度分子动力学 3D 折叠模拟和离子介导静电相互作用的蒙特卡罗紧束缚离子估计相结合。该模型预测不同盐条件下不同 RNA 发夹形成序列的自由能景观。理论预测结果与实验荧光测量结果一致，验证了该策略。此外，该理论模型超越了实验结果，能够进行深入的 3D 结构分析，揭示了序列和盐依赖性折叠稳定性的能量机制。虽然这里介绍的计算框架是为 RNA 发夹系统开发的，但通用方法可用于研究其他 RNA 系统，例如混合金属离子溶液中的多路连接或假结。