title: 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.
abstract: 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.
authors.affiliation: Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors.forename: Kosuke Ramon
authors.initials: KR
authors.lastname: Ito
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Kodama
authors.forename: Masaharu
authors.initials: M
authors.lastname: Tomizu
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Negoro
authors.forename: Ayako
authors.initials: A
authors.lastname: Orita
authors.forename: Tomohisa
authors.initials: T
authors.lastname: Osaki
authors.forename: Noritsugu
authors.initials: N
authors.lastname: Hosoki
authors.forename: Takaya
authors.initials: T
authors.lastname: Tanaka
authors.forename: Takeshi
authors.initials: T
authors.lastname: Imanishi
authors.forename: Satoshi
authors.initials: S
authors.lastname: Obika
mesh_terms: D020137:Base Pair Mismatch; D001952:Bridged-Ring Compounds / Q000737:chemistry; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D009584:Nitrogen / Q000737:chemistry; D009696:Nucleic Acids / Q000138:chemical synthesis / Q000737:chemistry; D010710:Phosphates / Q000737:chemistry; D017422:Sequence Analysis, DNA
chemical_list: D001952:Bridged-Ring Compounds; D009696:Nucleic Acids; D010710:Phosphates; C051802:triplex DNA; D004247:DNA; D009584:Nitrogen