Double-stranded DNA-templated cleavage of oligonucleotides containing a P3'-N5' linkage triggered by triplex formation: the effects of chemical modifications and remarkable enhancement in reactivity
| Autor: | Masaharu Tomizu, Noritsugu Hosoki, Satoshi Obika, Yoshinori Negoro, Kosuke Ramon Ito, Tomohisa Osaki, Takaya Tanaka, Takeshi Imanishi, Tetsuya Kodama, Ayako Orita |
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| Rok vydání: | 2010 |
| Předmět: |
Bridged-Ring Compounds
Stereochemistry Oligonucleotide Base Pair Mismatch Nitrogen DNA Sequence Analysis DNA Biology Hydrogen-Ion Concentration Cleavage (embryo) Phosphates chemistry.chemical_compound Biochemistry chemistry Nucleic Acids Synthetic Biology and Chemistry Genetics Nucleic acid Bridged nucleic acid A-DNA Cytokinesis |
| Zdroj: | Nucleic Acids Research |
| ISSN: | 1362-4962 |
| Popis: | We recently reported double-stranded DNA-templated cleavage of oligonucleotides as a sequence-specific DNA-detecting method. In this method, triplex-forming oligonucleotides (TFOs) modified with 5'-amino-2',4'-BNA were used as a DNA-detecting probe. This modification introduced a P3'→N5' linkage (P-N linkage) in the backbone of the TFO, which was quickly cleaved under acidic conditions when it formed a triplex. The prompt fission of the P-N linkage was assumed to be driven by a conformational strain placed on the linkage upon triplex formation. Therefore, chemical modifications around the P-N linkage should change the reactivity by altering the microenvironment. We synthesized 5'-aminomethyl type nucleic acids, and incorporated them into TFOs instead of 5'-amino-2',4'-BNA to investigate the effect of 5'-elongation. In addition, 2',4'-BNA/LNA or 2',5'-linked DNA were introduced at the 3'- and/or 5'-neighboring residues of 5'-amino-2',4'-BNA to reveal neighboring residual effects. We evaluated the triplex stability and reaction properties of these TFOs, and found out that chemical modifications around the P-N linkage greatly affected their reaction properties. Notably, 2',5'-linked DNA at the 3' position flanking 5'-amino-2',4'-BNA brought significantly higher reactivity, and we succeeded in indicating that a TFO with this modification is promising as a DNA analysis tool. |
| Databáze: | OpenAIRE |
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