Metal ion binding to catalytic RNA molecules

Cations play critical roles in ribozyme structure and catalysis. Unraveling the contributions of cations as catalytic cofactors is a complex process, due to their role in inducing RNA folding and their potential ability to influence chemical reactions. Recent studies have made progress in separating these roles by directly comparing ion-induced folding with ribozyme activity. In addition, spectroscopic studies have allowed some ribozyme metal sites to be directly observed in solution, providing binding affinities and ligand information. The emerging picture suggests that important cation sites can be classified according to their affinities and properties, and can be located within the ribozyme structure. At moderate ionic strengths, a common theme is emerging for some ribozymes of structural sites that have relatively high metal ion affinities and a second type of metal site with weaker affinity that is responsible for catalysis or structural fine-tuning. In the larger ribozymes, apparent clusters of metal-sensitive positions are observed.