3.21 - Metal-Ion Interactions with Nucleic Acids and Their Constituents

Abstract

This chapter focuses on the interaction of metal ions mainly with RNA and its building blocks. Metal ions are key to folding, structure, and function of any nucleic acid. These interactions are generally of a weak and highly dynamic nature as they concern mostly K+ and Mg2+ in living organisms. Aside from the large excess of loosly bound ions for charge compensation, a network of innersphere and outersphere interactions holds more specifically bound ions in place. For example, the affinity of metal ions toward ribose-hydroxyl groups is very small, but crucial for catalysis in ribozymes: This interaction is only enabled by the presence of a stronger primary binding site, which holds the metal ion in place. Such coordination on the atomic level is rather well characterized for the building blocks, but metal-ion binding to larger RNAs is much more complicated. After some general consideration, in the first part of this chapter, we summarize the accumulated knowledge on metal-ion binding to nucleobases, nucleotides, and dinucleotides, including also some rare nucleoside analogs. In the second part, the thermodynamics of metal-ion binding to RNA and known metal-ion binding motifs in RNA are described. Finally also today's knowledge on the role of metal ions in catalysis and folding of ribozymes and other large RNAs is summarized.