RNA Structure: Roles of Divalent Metal Ions

Abstract

Divalent metal ions play an important role in charge neutralization and incorrectly folding RNA into its three‐dimensional structure. They also play a potentially important role in the catalytic activity of RNA.

Keywords: RNA; divalent metal ions; catalysis; structure and folding; thermodynamics

Figure 1.

The high‐resolution crystal structure of transfer RNA and bound divalent metal ions. The sites that can bind magnesium are shown in blue, the site that can bind cobalt or magnesium is shown in orange, the site that can bind magnesium, manganese or cobalt is shown in magenta and the site that binds magnesium, manganese, zinc, cobalt or lead is shown in yellow.

Figure 2.

The four possible modes of RNA catalysis using divalent metal ions. (a) General base catalysis; (b) Lewis acid (electrophilic) catalysis; (c) leaving group activation; (d) nucleophilic activation.

Figure 3.

The crystal structure of the P5–P6 domain of the Tetrahymena thermophila group I intron showing the magnesium core. (The magenta sites are cobalt hexamine sites in the crystal structure, which are analogous to hexahydrated magnesium.)

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References

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Further Reading

Gesteland RF, Cech TR and Atkins JF (eds)(1993) The RNA World,2nd edn.New York: Cold Spring Harbor Press.

Gesteland RF and Atkins JF (eds)(1999) The RNA World. New York: Cold Spring Harbor Press.

Hanna R and Doudna JA (2000) Metal ions in ribozyme folding and catalysis. Current Opinion in Chemical Biology4: 166–170.

Nucleic Acid Database (NDB)(2001)[ http://ndbserver.rutgers.edu ]

Protein Data Bank (PDB) (2001)[ http://www.rcsb.org/pdb/index.html ]

Tinoco I Jr and Bustamante C (1999) How RNA Folds. Journal of Molecular Biology293: 271–281.

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How to Cite close
Carter, Richard J, and Holbrook, Stephen R(Feb 2003) RNA Structure: Roles of Divalent Metal Ions. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0003136]