Fig. 1.

The effect of pH and D₂O on cleavage rate. (A) Rate vs. pL (pH or pD) profiles of RG in H₂O (filled circles), RG in D₂O (open circles), RGkV in H₂O (filled diamonds), and RGkV in D₂O (open diamonds). (B) pL (pH or pD) profiles of 756C in H₂O (filled squares) and in D₂O (open squares). See Materials and Methods and Fig. 5 for a description of RNAs and mutants. The apparent first-order rate constant for cleavage (k_obs) is plotted as a function of pL at 37°C (see Materials and Methods). (C) Kinetic model for self-cleavage of an RNA, R, which contains a single general acid of the functional form HA⁺ and single general base of the functional form B⁻. The extent of protonation of the acid and base is determined by their pK_a values: pK_aA and pK_aB, respectively (from ref. 18). This model assumes the protonation states of the acid and base do not influence each other and that products (P) are only formed from RNA molecules in which both the general acid and base are in their active forms, _H+AR_B− (1); the proportion of RNA in this active form is abbreviated as f_R(1). k₁ is the intrinsic cleavage rate constant of the bond breaking step. Apparent pK_a values for RG and 756C RNAs were estimated by fitting data to the equation k_obs = f_R(1) × k₁ = k₁/[1 + 10^(pKaB−pH) + 10^{(pKaB−pKaA)} + 10^(pH−pKaA)] (18).