Isolation of synchronized E. coli elongation complexes for solid-phase and solution-based in vitro transcription assays

Synchronized transcription elongation complexes (TECs) are a fundamental tool for investigating the biochemical properties of RNA polymerases (RNAPs) and nascent RNA. We recently developed a standardized system for isolating high-purity synchronized E. coli RNAP TECs from an in vitro transcription reaction. Our system uses a custom 5’ leader sequence, called C3-SC1 to immobilize synchronized TECs on magnetic beads so that free DNA and non-productive transcription complexes can be depleted. The synchronized elongation complexes isolated by our procedure, called ^C3-SC1TECs, are > 98% active, > 95% pure, and can be used in both solid-phase and solution-based transcription assays. The yield of the procedure relative to input DNA is ~ 11% when ^C3-SC1TECs are isolated for solid-phase assays and ~ 8% when ^C3-SC1TECs are isolated for solution-based assays. Here we describe protocols for purifying ^C3-SC1TECs, and for assessing the activity, homogeneity, and yield of ^C3-SC1TEC preparations.