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

In vivo modification of different rRNAs by EDC and ETC. (A) Escherichia coli 16S rRNA, (B) Bacillus subtilis 5S rRNA, and (C) B. subtilis 23S rRNA probed with the indicated concentrations of EDC and ETC, and the corresponding structure with mapped reactivities. (Top panels) Ten percent denaturing PAGE. Dideoxy sequencing lanes (A,C,G,U) and an untreated control (0) are provided. Nucleotide labels to the left refer to the sequencing ladder, whereas labels to the right indicate significantly modified nucleotides. (Bottom panels) Pencils indicate reactivity values at each probing condition, where “SD” represents reactivity as a number of standard deviations away from the average signal of unmodified nucleotides. Gray nucleotides indicate regions without probing data.