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. 2003 Aug;9(8):907–918. doi: 10.1261/rna.5680603

FIGURE 4.

FIGURE 4.

Mechanism of RNA cleavage at low pH. In the range of pH 1 to 2, the rate constant for RNA cleavage is dependent on two protonations. These may represent specific acid β (purple) and δ (green) catalysis (upper pathway; monoanion phosphorane mechanism) or specific acid β catalysis with another protonation at the second NBPO (lower pathway; neutral phosphorane mechanism). Only the chemical structure of the RNA linkage that is directly involved in the transformation is depicted. The apical bonds to the pentacoordinated phosphorous in the trigonal, bipyramidal structure are indicated with dotted lines. Deprotonation of the 2′-oxygen nucleophile would be required in the lower pathway to prevent it from departing more readily than the 5′-oxygen atom. The upper and lower pathways will be kinetically indistinguishable if deprotonation of the 2′ oxygen in the neutral phosphorane is more rapid than cleavage of the P-O5′ bond, and protonation also occurs at the 5′ oxygen.