Catalytic Strategies

Among the various small, self-cleaving ribozymes, a variety of specific mechanisms may be used to achieve a similar set or subset of catalytic strategies. Those strategies include bringing the attacking group oxygen and phosphorus atoms into proximity and aligning those atoms with the leaving group oxygen atom, stabilizing the negative charge that develops in the transition state, and enhancing both the nucleophilicity of the 2' hydroxyl group and the leaving ability of the 5' oxygen. The HDV ribozymes have provided a good system to explore the potential for nucleobases or side chains of the RNA to act as general-acid-base catalysts (Fig. 2b,c).

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