Dinucleoside polyphosphates (Np_nNs) were discovered 50 years ago in all cells. They are often called alarmones, even though the molecular target of the alarm has not yet been identified. Recently, we showed that they serve as noncanonical initiating nucleotides (NCINs) and fulfill the role of 5′ RNA caps in Escherichia coli. Here, we present molecular insight into their ability to be used as NCINs by T7 RNA polymerase in the initiation phase of transcription. In general, we observed Np_nNs to be equally good substrates as canonical nucleotides for T7 RNA polymerase. Surprisingly, the incorporation of Ap_nGs boosts the production of RNA 10-fold. This behavior is due to the pairing ability of both purine moieties with the −1 and +1 positions of the antisense DNA strand. Molecular dynamic simulations revealed noncanonical pairing of adenosine with the thymine of the DNA.

中文翻译：

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双核苷多磷酸酯作为RNA构造模块，具有转录起始配对能力。

50年前在所有细胞中发现了双核苷多磷酸盐（Np _n Ns）。即使尚未确定警报的分子目标，它们也通常被称为警报器。最近，我们证明了它们可作为非常规起始核苷酸（NCIN），并在大肠杆菌中发挥5'RNA帽的作用。在这里，我们介绍了分子对它们在转录起始阶段被T7 RNA聚合酶用作NCIN的能力的洞察力。通常，我们观察到Np _n Ns与T7 RNA聚合酶的规范核苷酸一样具有良好的底物。令人惊讶的是，AP _n的合并Gs将RNA的产量提高了10倍。此行为归因于两个嘌呤部分与反义DNA链的-1和+1位的配对能力。分子动力学模拟揭示了腺苷与DNA胸腺嘧啶的非经典配对。