PATTERNS OF CLEAVAGES INDUCED BY LEAD IONS IN DEFINED RNA SECONDARY STRUCTURE MOTIFS

We have characterized the susceptibility of various RNA bulges, loops and other single-stranded sequences to hydrolysis promoted by Pb2+. Th e reactivity of bulges depends primarily on the structural context of the flanking base-pairs and the effect of nucleotide present at the 5' side of the bulge is particularly strong. The efficiency of stacking interactions between the bulged residue and its neighbors seems to det ermine cleavage specificity and efficiency. Hydrolysis of two-and thre e-nucleotide bulges depends only slightly on their nucleotide composit ion. In the case of terminal loops, the efficiency of their hydrolysis usually increases with the loop size and strongly depends on its nucl eotide composition. Stable tetraloops UUCG, CUUG and GCAA are resistan t to hydrolysis, while in some other loops of the GNRA family a single , weak cleavage occurs, suggesting the existence of structural subclas ses within the family. A very efficient, specific hydrolysis of a phos phodiester bond in the single-stranded region adjacent to the stem in oligomer 12 resembles highly specific cleavages of some tRNA molecules . The reaction occurs in the presence of Pb2+, but not in the presence of several other metal ions. The Pb2+-cleavable RNA domain may be con sidered another example of lead-zyme. The results of Pb2+-induced hydr olysis in model RNA oligomers should be useful in interpretation of cl eavage patterns of much larger, naturally occurring RNA molecules. (C) 1998 Academic Press Limited.