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Thermodynamic and kinetic modeling of transcriptional pausing

机译：转录暂停的热力学和动力学建模

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摘要

We present a statistical mechanics approach for the prediction of backtracked pauses in bacterial transcription elongation derived from structural models of the transcription elongation complex (EC). Our algorithm is based on the thermodynamic stability of the EC along the DNA template calculated from the sequence-dependent free energy of DNA-DNA, DNA-RNA, and RNA-RNA base pairing associated with (ⅰ) the translocational and size fluctuations of the transcription bubble; (ⅱ) changes in the associated DNA-RNA hybrid; and (ⅲ) changes in the cotranscriptional RNA secondary structure upstream of the RNA exit channel. The calculations involve no adjustable parameters except for a cutoff used to discriminate paused from nonpaused complexes. When applied to 100 experimental pauses in transcription elongation by Escherichia coli RNA polymerase on 10 DNA templates, the approach produces statistically significant results. We also present a kinetic model for the rate of recovery of backtracked paused complexes. A crucial ingredient of our model is the incorporation of kinetic barriers to backtracking resulting from steric clashes of EC with the cotrans-criptionally generated RNA secondary structure, an aspect not included explicitly in previous attempts at modeling the transcription elongation process.
机译：我们提出了一种统计力学方法，用于预测从转录延伸复合体（EC）的结构模型得出的细菌转录延伸中回溯的停顿。我们的算法基于EC沿着DNA模板的热力学稳定性，该模板是根据DNA-DNA，DNA-RNA和RNA-RNA碱基对与（ⅰ）的易位和大小波动相关的序列依赖性自由能计算得出的转录气泡（ⅱ）相关的DNA-RNA杂交体的变化； （ⅲ）RNA出口通道上游共转录RNA二级结构的变化。除了用于区分已暂停和未暂停的复合体的临界值外，计算不包含任何可调整的参数。当将大肠杆菌RNA聚合酶对10个DNA模板的转录延伸进行100次实验暂停时，该方法产生了统计上显着的结果。我们还提出了回溯的暂停复合物的恢复速率的动力学模型。我们模型的重要组成部分是将EC的空间冲突与共转录产生的RNA二级结构结合在一起的动力学障碍，以回溯，这是先前在模拟转录延伸过程中未曾明确涉及的一个方面。

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