Specificity and mechanism of the cleavages induced in yeast tRNAPhe by magnesium ions

The specificity of magnesium ion-induced hydrolysis of yeast tRNAPhe in solution was studied as a function of the excess of Mg(II) ions and pH. The major cuts at phosphates 16 and 20 as well as minor cleavages at phosphates 17, 18, 21, 34 and 36 occur at all pH values in the range of 8.0-9.5, and at a molar excess of magnesium ions over the tRNA ranging from 125 to 5000. In yeast tRNA(Phe)-Y the efficiency of the anticodon and D-loop cleavages is considerably decreased while the differently modified Y-base of yellow lupin tRNA(Phe) lowers the specificity of the weak anticodon loop cleavages. The mechanism of the Mg(II)-induced cleavages is discussed on the basis of yeast tRNA(Phe) crystal structure data, and the two major D-loop cleavages are thought to be effected from two distinct magnesium binding sites. The possibility of probing the environments of magnesium binding sites in tRNAs by the induced cleavages is demonstrated, and the relevance of magnesium-induced tRNA cleavages to RNA catalysis is discussed.