A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS

Carbodiimide in vivo and in vitro degradation assays. (A) The three carbodiimides used in this study: CMCT, EDC, and ETC. The quaternary amine of CMCT leads to a permanent positive charge and, thus, the counterion (p-toluene sulfonate) is present alongside the carbodiimide. Likewise, ETC has a counterion (iodide). EDC is shown in its neutral form, although a sizeable fraction is protonated at the amine. (B) Total RNA from Escherichia coli and Bacillus subtilis treated in vivo with EDC and ETC, visualized by 1% agarose gels. (C) 5′-end-labeled Saccharomyces cerevisiae tRNA^Phe treated in vitro with EDC, CMCT, and ETC. (D) 5′-end-labeled E. coli TPP riboswitch treated with EDC and CMCT. Both C and D are 10% denaturing PAGE, with percent degradation, “% deg,” provided at the bottom.