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. 2003 Aug;9(8):949–957. doi: 10.1261/rna.5670703

FIGURE 2.

FIGURE 2.

Representative examinations of the kinetic characteristics of RNA-cleaving ribozymes and deoxyribozymes. Plots 1 through 3 depict the assay data used to determine the optimal reaction conditions at pH 7.5 and 23°C with regard to the concentration (c) of enzyme, monovalent ion, and cofactor, respectively. Dashed lines identify the concentration of enzyme or cofactor needed to attain half-maximal kobs. Solid lines reflect theoretical activity curves generated using the maximum kobs and the KD values derived from plots 1 and 3. Optimization reactions for HD3 progressed as follows: plot 1 (500 mM KCl, 20 mM L-histidine); plot 2 (100 nM enzyme, 20 mM L-histidine); plot 3 (100 nM enzyme, 1 M KCl). Note: the methyl ester of histidine (HME) was used in place of histidine in plot 3 to increase cofactor solubility (Roth and Breaker 1998). Optimization reactions for MR11 progressed as follows: plot 1 (250 mM KCl, 20 mM MgCl2); plot 2 (100 nM enzyme, 20 mM MgCl2); plot 3 (100 nM enzyme, 500 mM KCl).