title: SRP RNA U21C mutant cotranscriptional folding, Replicate 2
design: DNA templates were prepared that consisted of an E. coli promoter followed by variable length RNA insert followed by an EcoRI site (GAATTC). DNA Template library was incubated with EcoRI E111Q mutant after creating open complexes with E. coli RNA polymerase, followed by initiating in vitro transcription with the addition of Mg++. Reactions were run for 30s at 37C in standard transcription buffer. Reactions were then probed with BzCN, or a control solvent (DMSO), prior to extraction with Trizol. Extracted RNAs were then processed according to the SHAPE-Seq v2.1 protocol for cDNA synthesis and library preparation prior to sequencing (doi:10.1016/j.ymeth.2016.04.002).