Complete identification of nonbridging phosphate oxygens involved in hammerhead cleavage

Phosphorothioate interference analysis is suited for the rapid identification of structurally and functionally important phosphate groups. Previous interference studies, however, have been limited to the analysis of pro-Rp phosphate oxygens. We employed solid-phase oligonucleotide synthesis and modification interference analysis to investigate either of the nonbridging phosphate oxygens within the hammerhead ribozyme. Two novel sites of Sp phosphorothioate interference were identified at positions A6 and U16.1. The results from interference experiments were confirmed by single phosphorothioate substitutions at sites of interest. Metal rescue experiments revealed that direct metal ion coordination occurs in the functional ribozyme only at the site of cleavage and at the pro-Rp oxygen of position Ag. The new approach may be generally useful in rapidly evaluating the functional importance of phosphate groups in nucleic acids.