Double-stranded DNA-templated cleavage of oligonucleotides containing a P3' arrow right N5' linkage triggered by triplex formation: the effects of chemical modifications and remarkable enhancement in reactivity

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&#...

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Bibliographic Details
Published inNucleic acids research Vol. 38; no. 20; pp. 7332 - 7342
Main Authors Ito, Kosuke Ramon, Kodama, Tetsuya, Tomizu, Masaharu, Negoro, Yoshinori, Orita, Ayako, Osaki, Tomohisa, Hosoki, Noritsugu, Tanaka, Takaya, Imanishi, Takeshi, Obika, Satoshi
Format Journal Article
LanguageEnglish
Published 01.01.2010
Subjects
Chemical modification
Microenvironments
nucleic acids
Oligonucleotides
Probes
Residual effects
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Summary: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' arrow right 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.
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ISSN:1362-4962