RT Journal Article SR Electronic T1 Purification of synchronized E. coli transcription elongation complexes by reversible immobilization on magnetic beads JF bioRxiv FD Cold Spring Harbor Laboratory SP 2022.01.10.475675 DO 10.1101/2022.01.10.475675 A1 Kelly, Skyler L. A1 Szyjka, Courtney E. A1 Strobel, Eric J. YR 2022 UL http://biorxiv.org/content/early/2022/01/10/2022.01.10.475675.abstract AB Synchronized transcription elongation complexes (TECs) are a fundamental tool for in vitro studies of transcription and RNA folding. Transcription elongation can be synchronized by omitting one or more NTPs from an in vitro transcription reaction so that RNA polymerase can only transcribe to the first occurrence of the omitted nucleotide(s) in the coding DNA strand. This approach was developed over four decades ago and has been applied extensively in biochemical investigations of RNA polymerase enzymes, but has not been optimized for RNA-centric assays. In this work, we describe the development of a system for isolating synchronized TECs from an in vitro transcription reaction. Our approach uses a custom 5’ leader sequence, called C3-SC1, to reversibly capture synchronized TECs on magnetic beads. We first show that complexes isolated by this procedure, called C3-SC1TECs, are >95% pure, >98% active, highly synchronous (94% of complexes chase in <15s upon addition of saturating NTPs), and compatible with solid-phase transcription; the yield of this purification is ∼8%. We then show that C3-SC1TECs perturb, but do not interfere with, the function of ZTP-sensing and ppGpp-sensing transcriptional riboswitches. For both riboswitches, transcription using C3-SC1TECs improved the efficiency of transcription termination in the absence of ligand but did not inhibit ligand-induced transcription antitermination. Given these properties, C3-SC1TECs will likely be useful for developing biochemical and biophysical RNA assays that require high-performance, quantitative bacterial in vitro transcription.Competing Interest StatementThe authors have declared no competing interest.RNAPRNA polymeraseTECtranscription elongation complexC3capture sequence 3SC1structure cassette 1etheno-dA1,N6-etheno-2’deoxyadenosineZMP5-aminoimidazole-4-carboxamide-1-β-D-ribofuranosyl 5’-monophosphateppGppguanosine-3’,5’-bisdiphosphateTBEtris-borate-EDTAPpelletSsupernatantTterminatedRTreadthrough