title: Use of RNA polymerase molecular beacon assay to measure RNA polymerase interactions with model promoter fragments.
abstract: RNA polymerase-promoter interactions that keep the transcription initiation complex together are complex and multipartite, and formation of the RNA polymerase-promoter complex proceeds through multiple intermediates. Short promoter fragments can be used as a tool to dissect RNA polymerase-promoter interactions and to pinpoint elements responsible for specific properties of the entire promoter complex. A recently developed fluorometric molecular beacon assay allows one to monitor the enzyme interactions with various DNA probes and quantitatively characterize partial RNA polymerase-promoter interactions. Here, we present detailed protocols for the preparation of an Escherichia coli molecular beacon and its application to study RNA polymerase interactions with model promoter fragments.
authors: Waksman Institute of Microbiology, Rutgers, State University of New Jersey, Piscataway, NJ, 08854, USA, mekler@waksman.rutgers.edu.
authors: Vladimir
authors: V
authors: Mekler
authors: Konstantin
authors: K
authors: Severinov
mesh_terms: D001483:Base Sequence; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics*; D005470:Fluorometry / Q000379:methods*; D008958:Models, Molecular; D015336:Molecular Probe Techniques; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics / Q000502:physiology*
chemical_list: D012321:DNA-Directed RNA Polymerases