title: RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions.
abstract: The molecular details of formation of transcription initiation complex upon the interaction of bacterial RNA polymerase (RNAP) with promoters are not completely understood. One way to address this problem is to understand how RNAP interacts with different parts of promoter DNA. A recently developed fluorometric RNAP molecular beacon assay allows one to monitor the RNAP interactions with various unlabeled DNA probes and quantitatively characterize partial RNAP-promoter interactions. This paper focuses on methodological aspects of application of this powerful assay to study the mechanism of transcription initiation complex formation by Escherichia coli RNA polymerase σ(70) holoenzyme and its regulation by bacterial and phage encoded factors.
authors.affiliation: Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA. Electronic address: mekler@waksman.rutgers.edu.
authors.forename: Vladimir
authors.initials: V
authors.lastname: Mekler
authors.affiliation: Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA; Skolkovo Institute of Science and Technology, 143025 Skolkovo, Russia; Institutes of Gene Biology and Molecular Genetics, Russian Academy of Sciences, 119334 Moscow, Russia. Electronic address: severik@waksman.rutgers.edu.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Severinov
mesh_terms: D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics*; D004926:Escherichia coli / Q000201:enzymology; D005470:Fluorometry; D008958:Models, Molecular; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D012321:DNA-Directed RNA Polymerases
keywords: Fluorescence spectroscopy; RNA polymerase; RNA polymerase–promoter interactions; Transcription initiation; Transcription regulation