Mechanisms of RNA SHAPE chemistry. (A) Stabilization of the intermediate reactive 2'-oxyanion. In the five superimposed hyper-reactive nucleotides, the non-bridging oxygen groups of the backbone (and the permanent charge) are directed away from the 2'-OH group. (B) General base catalysis. Examples of catalysis by the pyrimidine O2, purine N3, pro-S oxygen, and through-space groups are shown. For each panel, the number of occurrences observed in SHAPE analysis of 16S rRNA in crystallo is given in parentheses.