Miropolskaya Nataliya, Feklistov Andrey, Nikiforov Vadim, Kulbachinskiy Andrey
Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia.
The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
Biochem Biophys Res Commun. 2018 Jan 1;495(1):110-115. doi: 10.1016/j.bbrc.2017.10.151. Epub 2017 Oct 31.
Bacterial RNA polymerase (RNAP) is an RNA-synthesizing molecular machine and a target for antibiotics. In transcription, RNAP can interact with DNA sequence-specifically, during promoter recognition by the σ-containing holoenzyme, or nonspecifically, during productive RNA elongation by the core RNAP. We describe high-affinity single-stranded DNA aptamers that are specifically recognized by the core RNAP from Thermus aquaticus. The aptamers interact with distinct epitopes inside the RNAP main channel, including the rifamycin pocket, and sense the binding of other RNAP ligands such as rifamycin and the σ subunit. The aptamers inhibit RNAP activity and can thus be used for functional studies of transcription and development of novel RNAP inhibitors.
细菌RNA聚合酶（RNAP）是一种合成RNA的分子机器，也是抗生素的作用靶点。在转录过程中，RNAP可以在含σ的全酶识别启动子时与DNA进行序列特异性相互作用，也可以在核心RNAP进行有效的RNA延伸过程中进行非特异性相互作用。我们描述了高亲和力的单链DNA适体，它们能被嗜热栖热菌的核心RNAP特异性识别。这些适体与RNAP主通道内的不同表位相互作用，包括利福平口袋，并能感知其他RNAP配体如利福平和σ亚基的结合。这些适体抑制RNAP活性，因此可用于转录的功能研究和新型RNAP抑制剂的开发。
