Preparation and nuclease activity of hybrid "metallotris(methylpyridinium)porphyrin oligonucleotide" molecules having a 3'-loop for protection against 3'-exonucleases.

A 5'-GCGAAAGC minihairpin structure was added to the 3'-end of an oligonucleotide substituted at the 5'-end by a manganese cationic porphyrin in order to enhance the 3'-exonuclease resistance of these cleaver-antisense molecules. The influence of this minihairpin on the 3'-exonuclease resistance, the binding affinity to a target ssDNA, and the cleaving efficiency of Mn-cationic porphyrin oligonucleotide conjugates was compared to that of the parent molecule without the 3'-hairpin. The results showed that the 3'-hairpin slightly decreased the binding affinity and consequently the cleaving efficiency of the conjugated molecule toward a target sequence, but the much higher nuclease resistance makes 3'-minihairpin-protected metalloporphyrin oligonucleotides good candidates as reactive antisense oligonucleotides for studies on cells.