The observed rates of ribozyme cleavage reactions are strongly dependent on the nature of the metal ion present. Metal ions can thereby exhibit a stronger inhibiting or accelerating effect compared to Mg(2+), which is usually considered the natural cofactor. Alkaline, alkaline earth, transition, d(10), and other metal ions are applied either to gain a spectroscopic handle on the metal center, and/or to elucidate the catalytic mechanism. Here we shortly review some of the most recent publications on the influence of different metal ions on catalysis of the hammerhead, hepatitis delta virus, and group II intron ribozymes. Comparison of the observed cleavage rates of hammerhead ribozymes with the metal ion affinities of different ligands reveals that these rates correlate perfectly with the intrinsic phosphate affinities of the metal ions involved.
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