The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK_a

Ionic environment determines the apparent pK _a of the general acid and general base and the observed rate of cleavage. (A) The logarithm of the maximal observed rate of cleavage in a given ionic condition, log₁₀k_obs^max, is plotted as a function of the absolute value of the difference between pK_aA and pK_aB (| ΔpK_a |). The solid line describes the theoretical relationship between ΔpK_a and log₁₀k_obs^max for a reaction catalyzed solely by general acid–base catalysis with k₁ = 5.8 × 10⁴ min⁻¹ (the mean of the estimates of k₁ in the four ionic conditions examined in Fig. 1; see Table 1). Dotted gridlines are included to emphasize the linear relationship between the y- and x-axis variables over most of the pH range. (B) log₁₀k_obs^max is plotted as a function of the values of pK _aA (open symbols) or pK _aB (filled symbols) in Mg²⁺ (○); Mn²⁺ (▽); Mg²⁺+Li⁺ (△); Li⁺ (□) NH₄⁺ (∗); and Na⁺ (⋄). Symbols for NH₄ ⁺ and Na⁺ lie on top of each other in B. Error bars indicate the upper and lower range of pK _a estimates including uncertainties from all sources (see Materials and Methods); error bars in A are the sum of the error bars in B. pK _aB could not be experimentally determined for some cations due to oxidation of the metal ion, RNA degradation, or buffering by the metal ion at high pH (see Materials and Methods).