Chemical nucleases: their use in studying RNA structure and RNA-protein interactions

Metal complexes that cleave nucleic acids provide a new means to study RNA structure and RNA-protein interactions. Methods that use these chemical nucleases help compensate for the limitations of other techniques used to determine structure. Because the ligands that coordinate the metal generally control the cleavage selectivity of these complexes, it has become possible to design nucleolytic reagents that target specific higher-order structures. In combination with site-directed mutagenesis these conformation-specific probes can be used to delineate long-range interactions. Alternatively, complexes that cut irrespective of sequence and secondary structure have been used in protection (foot-printing) experiments to locate protein binding sites. Because each position of the nucleic acid is susceptible to cleavage, the protection pattern yields a highly resolved definition of the contact site between the protein and RNA. In other applications, metal complexes have been conjugated to functional moieties such as oligonucleotides, peptides, or substrate analogs to direct their binding to a distinct site on a specific RNA molecule. This latter strategy holds significant therapeutic promise for the destruction of pathogenic RNAs.