TRIPLEX-MEDIATED CLEAVAGE OF DNA BY 1,10-PHENANTHROLINE-LINKED 2'-O-METHYL RNA

We have previously reported that 2'-O-methyl RNAs are efficient probes for duplex DNA, Here we describe the design, synthesis, and DNA cleav ing activity of 1,10-phenanthroline (OP)-linked 2'-O-methyl RNA (OP-m) . Although a local triple helix was formed, both with OP-m and a contr ol OP-linked DNA at the target sequence of the duplex DNA, the promote r region of the human thrombomodulin gene, the cleavage efficiencies o n both strands were not proportional when OP-m was used as a cleavage agent. These results may reflect the structural differences of the res pective triple helices and the duplex-tripler junction, formed from th e two types of triplex-forming oligonucleotides, 2'-O-methyl RNA and D NA. Since the OF-ms were found to work as preferential purine-strand c utters for duplex DNA, they would be useful as unique tools for genome analysis.