Abstract
The nucleolytic ribozymes carry out site-specific RNA cleavage reactions by nucleophilic attack of the 2′-oxygen atom on the adjacent phosphorus with an acceleration of a million-fold or greater. A major part of this arises from concerted general acid–base catalysis. Recent identification of new ribozymes has expanded the group to a total of nine and this provides a new opportunity to identify sub-groupings according to the nature of the general base and acid. These include nucleobases, hydrated metal ions, and 2′-hydroxyl groups. Evolution has selected a number of different combinations of these elements that lead to efficient catalysis. These differences provide a new mechanistic basis for classifying these ribozymes.
Highlights
The nucleolytic ribozymes carry out site-specific RNA cleavage reactions by nucleophilic attack of the 2′-oxygen atom on the adjacent phosphorus with an acceleration of a million-fold or greater
This review focuses on a sub-group of the ribozymes where some general principles can be discerned
Some nucleolytic ribozymes certainly employ hydrated metal ions in their catalysis, the common theme among these species is the use of concerted general acid–base catalysis
Summary
The nucleolytic ribozymes carry out site-specific RNA cleavage reactions by nucleophilic attack of the 2′-oxygen atom on the adjacent phosphorus with an acceleration of a million-fold or greater. In the VS ribozyme, this has been measured at 8.428, where proximity of a bound metal ion likely reduces the pKa. Grouping the nucleolytic ribozymes While guanine acting as general base is very common, the general acid is rather more variable. Consideration of the general base and acid provides a way to group the nucleolytic ribozymes mechanistically (Table 1 and Figure 2).
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