Enhancing Sequence-Specific Cleavage of RNA within a Duplex Region:  Incorporation of 1,3-Propanediol Linkers into Oligonucleotide Conjugates of Serinol−Terpyridine

Abstract

The syntheses and RNA cleavage efficiencies of a new series of oligonucleotide conjugates of Cu(II)-serinol-terpyridine and 1,3-propanediol are reported. These reagents, termed ribozyme mimics, were designed such that they would yield multiple unpaired RNA residues directly opposite the site of the RNA 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 nucleotide. Incorporation of one or more of these 1,3-propanediol linkers at positions directly adjacent to the serinol-terpyridine modification in the ribozyme mimic DNA strand resulted in cleavage at multiple phosphates in a complementary 31-mer RNA target sequence. The linkers effectively created artificial mismatches in the RNA-DNA duplexes, rendering the opposing RNA residues much more susceptible to cleavage via the transesterification/hydrolysis pathway. The RNA cleavage products produced by the various mimics correlated directly with the number and locations of the linkers in their DNA strands, and the most active ribozyme mimic in the series exhibited multiple turnover in the presence of excess 31-mer RNA target.

Artificial ribonucleases

“…The half-life was, however, 400 h in excess of Cu 2+ -6 at pH 7.5 and 37 • C. The cleaving activity was later improved by tethering the cleaving agent to a serinol backbone unit (7) 44, 45 and inserting propane-1,3-diol spacers to both sides of the serinol unit. 46 Accordingly, a trinucleotide internal loop was formed at the cleavage site, which facilitated the cleavage. The half-life was in this manner reduced to 30 h at pH 7.4 and 45 • C, corresponding a half-life of about 40 h at pH 7.5 and 37 • C. The reaction also showed turnover in excess of the target.…”

Oxazolidine copper complexes: Synthesis, characterization and superoxide dismutase activity of copper(II) complexes with oxazolidine ligands derived from hydroxyquinoline carboxaldehyde

“…Two amines were selected to complete a series of ligands, serinol and ethanolamine. Serinol was used in the synthesis of some species of ceramides, acting as messengers for regulation and cellular apoptosis, an artificial nucleic acid and for DNA cleavage . Ethanolamine is widely used for adsorption and removal processes of carbon dioxide …”

Zinc Ion-Dependent Peptide Nucleic Acid-Based Artificial Enzyme that Cleaves RNA—Bulge Size and Sequence Dependence

“…Furthermore, the molecular environment within the RNA bulge, including the size, bulge sequence, stacking of the nucleobases, and orientation of the phosphodiester bonds within, has a considerable influence on the overall reactivity of the phosphodiester bonds. It is also preferable to cleave the target RNA in a central part of the RNA sequence so that RNA fragments can readily dissociate [ 17 , 18 , 19 ].…”