RNA polymerase molecular beacon as tool for studies of RNA polymerase-promoter interactions

Methods. 2015 Sep 15:86:19-26. doi: 10.1016/j.ymeth.2015.04.033. Epub 2015 May 5.

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.

Keywords: Fluorescence spectroscopy; RNA polymerase; RNA polymerase–promoter interactions; Transcription initiation; Transcription regulation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics*
  • DNA-Directed RNA Polymerases / chemistry
  • DNA-Directed RNA Polymerases / genetics*
  • Escherichia coli / enzymology
  • Fluorometry
  • Models, Molecular
  • Promoter Regions, Genetic*
  • Protein Binding
  • Transcription, Genetic*

Substances

  • DNA-Binding Proteins
  • DNA-Directed RNA Polymerases