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

Folding of the 16S 3′ major domain from Escherichia coli. (A) DMS reactivity at As and Cs and ETC reactivity at Gs and Us mapped onto the known structure. Reactivity values are provided in the legend. Nucleotides without reactivity values are gray. (B–E) Circle plots comparing the known structure to the predicted structure using (B) no pseudo-free energy restraints, (C) ETC reactivities at Gs and Us as restraints, (D) DMS reactivities at As and Cs as restraints, and (E) combined ETC and DMS reactivities as restraints. Incorrect base pairs are yellow, unpredicted base pairs are black, and correct base pairs are blue.