Max Planck Institute of Colloids and Interfaces, Science Park Golm, D-14424 Potsdam, Germany.
J Phys Condens Matter. 2013 Sep 18;25(37):374104. doi: 10.1088/0953-8984/25/37/374104. Epub 2013 Aug 15.
Transcription by RNA polymerases is frequently interrupted by pauses. One mechanism of such pauses is backtracking, where the RNA polymerase translocates backward with respect to both the DNA template and the RNA transcript, without shortening the transcript. Backtracked RNA polymerases move in a diffusive fashion and can return to active transcription either by diffusive return to the position where backtracking was initiated or by cleaving the transcript. The latter process also provides a mechanism for proofreading. Here we present some exact results for a kinetic model of backtracking and analyse its impact on the speed and the accuracy of transcription. We show that proofreading through backtracking is different from the classical (Hopfield-Ninio) scheme of kinetic proofreading. Our analysis also suggests that, in addition to contributing to the accuracy of transcription, backtracking may have a second effect: it attenuates the slow down of transcription that arises as a side effect of discriminating between correct and incorrect nucleotides based on the stepping rates.
RNA 聚合酶的转录经常被暂停打断。暂停的一种机制是回溯，在此过程中，RNA 聚合酶相对于 DNA 模板和 RNA 转录本向后移动，而不会缩短转录本。回溯的 RNA 聚合酶以扩散的方式移动，并且可以通过扩散回到回溯开始的位置，或者通过切割转录本，重新回到活跃的转录状态。后一种过程也为校对提供了一种机制。在这里，我们提出了一个回溯的动力学模型的一些精确结果，并分析了它对转录速度和准确性的影响。我们表明，通过回溯进行校对与经典的（Hopfield-Ninio）动力学校对方案不同。我们的分析还表明，回溯除了有助于转录的准确性之外，还可能产生第二个影响：它减轻了由于根据进入的核苷酸的进入速率区分正确和错误核苷酸而产生的转录速度减缓。
