A trinucleotide can promote metal ion-dependent specific cleavage of RNA.

Nucleotide sequence and metal ion requirements for Mn(2+)-dependent self-cleavage of an RNA 31 nucleotides long [Dange, V., Van Atta, R. B. & Hecht, S. M. (1990) Science 248, 585-588] were examined by analysis of the site-specific cleavage activity of substitution and deletion mutants as well as complexes assembled from fragments of this RNA. A complex of UUU and GAAACp allows specific cleavage between G and A at 37 degrees C and pH 7.5. Additional nucleotides flanking the oligonucleotides in the minimal complex are not necessary for the cleavage reaction to take place but can affect the rate of the reaction. The 2'-OH groups of uridine residues do not participate in catalysis since both poly(U) and poly(dU) can promote the specific cleavage reaction in trans. Cd2+ ions can also promote the specific cleavage reaction and Mg2+ ions (which are inactive alone), under certain conditions, can enhance the Mn(2+)-induced cleavage of RNA.