RNA unfolding and refolding are important biological phenomena, which occur during the transfer of genetic information from DNA to RNA to proteins. During these processes, RNA is found in single stranded, secondary and tertiary structures, including secondary conformations like hairpins and pseudoknots. Understanding the diverse conformations of RNA and how these influence the dynamics of unfolding and refolding is crucial to gain insight to fundamental biological processes. In this work, we employ coarse-grained Langevin dynamics simulations of a simple model of different RNA hairpins passing through a geometric nanopore to find the influence of structural changes on the translocation dynamics. The threshold voltage of unfolding depends on the length of the hairpin attached to the tail. The lag time to unfold is longer for smaller applied voltages and for the architectures containing a longer hairpin attached to the tail. Chain translocation dynamics for different architectures are largely collapsed by the threshold. A distinct signature for the base unfolding time was observed for the bases around the unpaired bases in all the RNA hairpin models. These results can motivate future technologies or experiments that use translocation to predict secondary structures of polynucleotides.

中文翻译：

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通过纳米孔易位展开RNA

RNA 解折叠和重折叠是重要的生物学现象，发生在遗传信息从 DNA 到 RNA 再到蛋白质的转移过程中。在这些过程中，RNA 存在于单链、二级和三级结构中，包括二级构象，如发夹和假结。了解 RNA 的不同构象以及这些构象如何影响展开和重折叠的动力学对于深入了解基本的生物过程至关重要。在这项工作中，我们对通过几何纳米孔的不同 RNA 发夹的简单模型进行粗粒度朗之万动力学模拟，以发现结构变化对易位动力学的影响。展开的阈值电压取决于连接到尾部的发夹的长度。对于较小的施加电压和包含连接到尾部的较长发夹的架构，展开的滞后时间较长。不同架构的链易位动态在很大程度上被阈值破坏了。对于所有 RNA 发夹模型中未配对碱基周围的碱基，观察到碱基展开时间的独特特征。这些结果可以激发未来使用易位来预测多核苷酸二级结构的技术或实验。