Double‐Stranded DNA‐Templated Oligonucleotide Digestion Triggered by Triplex Formation

Obika, Satoshi; Tomizu, Masaharu; Negoro, Yoshinori; Orita, Ayako; Nakagawa, Osamu; Imanishi, Takeshi

doi:10.1002/cbic.200700430

Cited by 10 publications

(18 citation statements)

References 34 publications

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“…This modification introduced a P–N linkage in the backbone of the TFO, instead of the P–O linkage generally found in phosphodiester moieties of oligonucleotides. Although it is well known that a P–N linkage is cleavable under mild acidic conditions (29), we found out that the cleaving reaction of the P–N linkage was greatly accelerated when the TFO formed a triplex with its target dsDNA in a sequence-specific manner under mild acidic conditions (Scheme 1A) (28,30). We demonstrated that this dsDNA-templated cleavage combined with fluorescence resonance energy transfer (FRET) technology was useful as a DNA detecting method, distinguishing a single nucleotide mismatch (28).…”

Section: Introductionmentioning

confidence: 90%

“…TFO′ and TFO* were prepared according to previous reports (28,29). Syntheses of TFO1–TFO9 were performed at a 0.2 µmol scale on an automated DNA synthesizer (Applied Biosystems, Expedite TM 8909) using the standard phosphoramidite protocol on CPG supports except for coupling time of certain couplings (90 s in the standard protocol).…”

Section: Methodsmentioning

confidence: 99%

“…We recently reported on a double-stranded DNA (dsDNA)-templated cleavage of oligonucleotides as a sequence-specific DNA detecting method (28). In this method, triplex-forming oligonucleotides (TFOs) modified with 5′-amino-2′- O ,4′- C -methylene bridged nucleic acid (5′-amino-2′,4′-BNA) were used (28).…”

Section: Introductionmentioning

confidence: 99%

“…In this method, triplex-forming oligonucleotides (TFOs) modified with 5′-amino-2′- O ,4′- C -methylene bridged nucleic acid (5′-amino-2′,4′-BNA) were used (28). This modification introduced a P–N linkage in the backbone of the TFO, instead of the P–O linkage generally found in phosphodiester moieties of oligonucleotides.…”

Section: Introductionmentioning

confidence: 99%

“…In a previous report, we proposed that the acid-mediated cleavage of the P–N linkage triggered by triplex formation should be driven by a conformational strain on the P–N linkage (28). This interested us in the effects of modifications in changing the microenvironment around the P–N linkage.…”

Section: Introductionmentioning

confidence: 99%

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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

Ito

Kodama

Tomizu

et al. 2010

Nucleic Acids Research

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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.

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