论文标题
RNA二级结构的共转录动力学折叠（包括伪诺）
Cotranscriptional kinetic folding of RNA secondary structures including pseudoknots
论文作者
论文摘要
RNA结构的计算预测是计算结构生物学中的重要问题。 RNA结构形成的研究通常假定该过程从完全合成的序列开始。但是，实验证据表明，RNA与其伸长率同时折叠。我们研究了包括伪诺（Pseudoknots）在内的RNA二级结构形成，这些结构考虑了共转录效应。我们提出了RNA分子折叠过程的单核苷酸分辨率动力学模型，其中将新核苷酸的聚合酶驱动的RNA链伸长作为原始操作包括在内，以及一种随机仿真方法，该方法与转录合成同时折叠。数值案例研究表明，我们的共转录RNA折叠模型可以预测实际生物系统中有利于的构象的形成。因此，我们的新计算工具可以提供定量预测，并为RNA折叠动力学提供有用的见解。
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence, however, has shown that RNA folds concurrently with its elongation. We investigate RNA secondary structure formation, including pseudoknots, that takes into account the cotranscriptional effects. We propose a single-nucleotide resolution kinetic model of the folding process of RNA molecules, where the polymerase-driven elongation of an RNA strand by a new nucleotide is included as a primitive operation, together with a stochastic simulation method that implements this folding concurrently with the transcriptional synthesis. Numerical case studies show that our cotranscriptional RNA folding model can predict the formation of conformations that are favored in actual biological systems. Our new computational tool can thus provide quantitative predictions and offer useful insights into the kinetics of RNA folding.
