Two recent theoretical models, Bai et al. (2004, 2007) and Tadigotla et al. (2006), formulated thermodynamic explanations of sequence-dependent transcription pausing by RNA polymerase (RNAP). The two models differ in some basic assumptions and therefore make different yet overlapping predictions for pause locations, and different predictions on pause kinetics and mechanisms. Here we present a comprehensive comparison of the two models. We show that while they have comparable predictive power of pause locations at low NTP concentrations, the Bai et al. model is more accurate than Tadigotla et al. at higher NTP concentrations. Pausing kinetics predicted by Bai et al. is also consistent with time-course transcription reactions, while Tadigotla et al. is unsuited for this type of kinetic prediction. More importantly, the two models in general predict different pausing mechanisms even for the same pausing sites, and the Bai et al. model provides an explanation more consistent with recent single molecule observations.

中文翻译：

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两种序列依赖性转录模型的暂停预测比较

两个最近的理论模型，Bai 等人。(2004, 2007) 和 Tadigotla 等人。(2006)，制定了 RNA 聚合酶 (RNAP) 对序列依赖性转录暂停的热力学解释。这两个模型在一些基本假设上有所不同，因此对暂停位置做出不同但重叠的预测，并对暂停动力学和机制做出不同的预测。在这里，我们对两种模型进行了全面的比较。我们表明，虽然它们在低 NTP 浓度下具有相当的暂停位置预测能力，但 Bai 等人。模型比 Tadigotla 等人更准确。在更高的 NTP 浓度下。Bai 等人 预测的暂停动力学。也与时程转录反应一致，而 Tadigotla 等人。不适合这种类型的动力学预测。更重要的是，这两个模型通常预测不同的暂停机制，即使对于相同的暂停站点也是如此，Bai 等人。模型提供了与最近的单分子观察结果更一致的解释。