Nucleobase catalysis in ribozyme mechanism.

RNA performs a wide range of functions in biology including catalysis of chemical reactions. A major goal in the field of ribozyme chemical biology is to understand these functions in molecular terms. There is increasing evidence that ribozymes can use their nucleobases directly in chemical catalysis in a variety of ways. These include hydrogen bonding to the transition state, stabilizing charge development, and transferring protons as general acid-base catalysts. This article highlights recent kinetic, structural, single molecule, and synthetic approaches that have been used to probe the roles of ribozyme nucleobases in phosphodiester bond cleavage.