Enhancing sequence-specific cleavage of RNA within a duplex region: Incorporation of 1,3-propanediol linkers into oligonucleotide conjugates of serinol-terpyridine

The syntheses and RNA cleavage efficiencies of a new series of oligonucleot ide conjugates of Cu(II)serinol-terpyridine and 1,3-propanediol are reporte d. These reagents, termed ribozyme mimics, were designed such that they wou ld yield multiple unpaired RNA residues directly opposite the site of the R NA cleavage catalyst upon ribozyme mimic-RNA duplex formation. This design effect was implemented using the 1,3-propanediol linker 3, which mimics the three-carbon spacing between the 5'- and 3'-hydroxyls of a natural nucleot ide. Incorporation of one or more of these 1,3-propanediol linkers at posit ions directly adjacent to the serinol-terpyridine modification in the riboz yme mimic DNA strand resulted in cleavage at multiple phosphates in a compl ementary 31-mer RNA target sequence. The linkers effectively created artifi cial mismatches, in the RNA-DNA duplexes, rendering the opposing RNA residu es much more susceptible to cleavage via the transesterification/hydrolysis pathway. The RNA cleavage products produced by the various mimics correlat ed directly with the number and locations of the linkers in their DNA stran ds, and the most active ribozyme mimic in the series exhibited multiple tur nover in the presence of excess 31-mer RNA target.