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12 Divalent Metal Ions in RNA Folding and Catalysis

Tao Pan, David M. Long, Olke C. Uhlenbeck


Approximately three-quarters of all chemical elements are metals. Metal ions associate with RNA in solution in a number of interesting ways. The highly water-soluble ionic forms of certain metal ions are abundant in seawater and inside cells and play vital roles in RNA folding and catalysis. In this chapter, we examine the role of divalent ions in RNA folding. The properties of a number of divalent metal ions are summarized, and experiments examining their binding to RNA in solution and crystals are evaluated. We also review the evidence that precisely placed metal ions can promote catalysis by RNA. Since the mechanisms of group I introns and RNase P are the subject of another chapter (Cech, this volume), we focus here on biological and nonbiological examples of catalytic cleavage of the RNA that give products containing 2′, 3′ -cyclic phosphate and 5′ -hydroxyl termini.

The concentrations of a number of metal ions in seawater and cells are given in Table 1. Intracellular metal ion concentrations vary widely and are maintained and adjusted by a variety of active and passive transport mechanisms. Inside cells, free metal ion concentrations are much lower than total metal ion concentrations, since intracellular macromolecules bind substantial amounts of metal ions.

Table 2 lists certain chemical properties of selected metal ions that are relevant to their interaction with RNA. In aqueous solutions, metal ions form coordination complexes with water or solutes. The coordination number (number of ligands that bind) and coordination geometry (geometric arrangement...

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