title: An isocytidine derivative with a 2-amino-6-methylpyridine unit for selective recognition of the CG interrupting site in an antiparallel triplex DNA.
abstract: Sequence-specific recognition of duplex DNA mediated by triple helix formation offers a potential basis for oligonucleotide therapy and biotechnology. However, triplex formation is limited mostly to homopurine strands, due to poor stabilization at CG or TA base pairs in the target duplex DNA sequences. Several non-natural nucleosides have been designed for the recognition of CG or TA base pairs within an antiparallel triplex DNA. Nevertheless, problems including low selectivity and high dependence on the neighboring bases remain unsolved. We thus synthesized N(2)-arylmethyl isodC derivatives and incorporated them into triplex-forming oligonucleotides (TFOs) for the selective recognition of the CG base pair within antiparallel triplex DNA. It was shown that an isodC derivative bearing a 2-amino-6-methylpyridine moiety (AP-isodC) recognizes the CG base pair with high selectivity in antiparallel triplex DNA irrespective of the flanking base pairs.
authors.affiliation: Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582 (Japan).
authors.forename: Hidenori
authors.initials: H
authors.lastname: Okamura
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Taniguchi
authors.forename: Shigeki
authors.initials: S
authors.lastname: Sasaki
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D003562:Cytidine / Q000737:chemistry*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D009690:Nucleic Acid Conformation; D011725:Pyridines / Q000737:chemistry*
chemical_list: D011725:Pyridines; C051802:triplex DNA; C083576:isocytidine; D003562:Cytidine; D004247:DNA; C023666:pyridine
keywords: CG base pair; DNA recognition; isocytidine; nucleosides; triplex DNA