Density- and elongation speed-dependent error correction in RNA polymerization
Density- and elongation speed-dependent error correction in RNA polymerization
复制标题
DOI：
10.1088/1478-3975/ac45e2
复制
发表时间：
2021-03
期刊：
影响因子：
2
通讯作者：
Xinzhe Zuo;T. Chou
中科院分区：
文献类型：
--
作者：
Xinzhe Zuo;T. Chou
RNA聚合酶的回溯（RNAP）是DNA转录过程中一种重要的暂停机制，是提高转录保真度的纠错过程的一部分。我们模拟RNAP的回溯机制，这通常发生在聚合酶试图将一个非同源或“错配”的核苷酸三磷酸。先前的模型已经做出了简化的假设，例如忽略回溯聚合酶后面的拖尾聚合酶或假设拖尾聚合酶是固定的。我们推导出精确的解析解的随机模型，其中包括本地相互作用的RNAP明确显示如何尾随RNAP影响的概率，错误被纠正或纳入领先的回溯RNAP。我们还提供了两个相关的方法来计算平均时间的错误校正和合并给定的初始本地RNAP配置。利用这些结果，我们提出了一个有效的相互作用RNAP晶格，可以很容易地模拟。
Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNAP, which usually happens when the polymerase tries to incorporate a noncognate or ‘mismatched’ nucleotide triphosphate. Previous models have made simplifying assumptions such as neglecting the trailing polymerase behind the backtracking polymerase or assuming that the trailing polymerase is stationary. We derive exact analytic solutions of a stochastic model that includes locally interacting RNAPs by explicitly showing how a trailing RNAP influences the probability that an error is corrected or incorporated by the leading backtracking RNAP. We also provide two related methods for computing the mean times for error correction and incorporation given an initial local RNAP configuration. Using these results, we propose an effective interacting-RNAP lattice that can be readily simulated.