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 cleaving 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 control OP-linked DNA at the target sequence of the duplex DNA, the promoter region of the human thrombomodulin gene, the cleavage efficiencies on both strands were not proportional when OP-M was used as a cleavage agent. These results may reflect the structural differences of the respective triple helices and the duplex-triplex junction, formed from the two types of triplex-forming oligonucleotides, 2'-O-methyl RNA and DNA. Since the OP-ms were found to work as preferential purine-strand cutters for duplex DNA, they would be useful as unique tools for genome analysis.
Shimizu
M
M
Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
Morioka
H
H
Inoue
H
H
Ohtsuka
E
E
D001483:Base Sequence; D001665:Binding Sites; D003432:Cross-Linking Reagents / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D015342:DNA Probes / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism; D006801:Humans; D008738:Methyl Ethers / Q000737:chemistry; D008969:Molecular Sequence Data; D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry; D010618:Phenanthrolines / Q000737:chemistry*; D010710:Phosphates / Q000737:chemistry; D011401:Promoter Regions, Genetic; D012313:RNA / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism; D015183:Restriction Mapping; D012260:Ribonucleases / Q000737:chemistry / Q000378:metabolism; D018180:Thrombomodulin / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
D003432:Cross-Linking Reagents; D015342:DNA Probes; D008738:Methyl Ethers; D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides; D010618:Phenanthrolines; D010710:Phosphates; D018180:Thrombomodulin; D012313:RNA; D004247:DNA; D012260:Ribonucleases; C035638:thiophosphoric acid; C025205:1,10-phenanthroline