Abstract：
Although RNA molecules are synthesized via transcription, little is known about the general impact of cotranscriptional folding in vivo. We present different computational approaches for the simulation of changing structure ensembles during transcription, including interpretations with respect to experimental data from literature. Specifically, we analyze different mutations of the E. coli SRP RNA, which has been studied comparatively well in previous literature, yet the details of which specific metastable structures form as well as when they form are still under debate. Here, we combine thermodynamic and kinetic, deterministic, and stochastic models with automated and visual inspection of those systems to derive the most likely scenario of which substructures form at which point during transcription. The simulations do not only provide explanations for present experimental observations but also suggest previously unnoticed conformations that may be verified through future experimental studies.
摘要：
尽管RNA分子是通过转录合成的，关于体内共转录折叠的一般影响知之甚少。我们提出了不同的计算方法来模拟转录过程中变化的结构集合，包括对文献中实验数据的解释。具体来说,我们分析了大肠杆菌SRPRNA的不同突变，这在以前的文献中得到了比较好的研究，然而，具体的亚稳态结构形成的细节以及它们何时形成仍在争论中。这里,我们结合了热力学和动力学，确定性，和随机模型，对这些系统进行自动和视觉检查，以得出最可能的情况，即在转录过程中的哪个点形成子结构。模拟不仅为当前的实验观察提供了解释，而且还提出了以前未被注意到的构象，这些构象可以通过未来的实验研究来验证。
