In situ footprinting of E. coli transcription elongation complex with chloroacetaldehyde

• Published in: Methods in molecular biology (Clifton, N.J.) Vol. 1276; p. 229
• Main Authors: Rahmouni, A Rachid, Mosrin-Huaman, Christine
• Format: Journal Article
• Language: English
• Published: United States 2015
• Subjects: Acetaldehyde - analogs & derivatives; DNA Footprinting - methods; Escherichia coli - genetics; Escherichia coli - physiology; Transcription Elongation, Genetic - physiology
• ISSN: 1940-6029
• DOI: 10.1007/978-1-4939-2392-2_13

The structure and dynamics of Escherichia coli transcription elongation complex are now well documented. However, most of the studies have been conducted in vitro and frequently under artificial conditions that facilitate the biochemical characterization of the complex. Thus, little is known about relevance of these results for the regulatory aspects of transcription elongation inside the cell. Here, we describe the use of a single-strand-specific probe chloroacetaldehyde for in situ footprinting of E. coli elongation complex temporarily halted by a protein roadblock. The method provides valuable information on the dynamic features of transcriptionally engaged RNA polymerase within the cellular environment.