title: New nucleotide pairs for stable DNA triplexes stabilized by stacking interaction.
abstract: New nucleotide pairs applicable to formation of DNA triplexes were developed. We designed oligonucleotides incorporating 5-aryl deoxycytidine derivatives (dC5Ars) and cyclic deoxycytidine derivatives, dCPPP and dCPPI, having an expanded aromatic area, as the second strand. As pairing partners, two types of abasic residues (C3: propylene linker, phi: abasic base) were chosen. It was concluded that, when the 5-aryl-modified cytosine bases paired with the abasic sites in TFOs in a space-fitting manner, the stability of the resulting triplexes significantly increased. The recognition of C3 toward dC5Ars was selective because of the stacking interactions between their aromatic part and the nucleobases flanking the abasic site. These results indicate the potential utility of new nucleotide triplets for DNA triplex formation, which might expand the variety of structures and sequences and might be useful for biorelated fields such as DNA nanotechnologies.
authors.affiliation: Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Midoriku, Yokohama 226-8501, Japan.
authors.forename: Masahiro
authors.initials: M
authors.lastname: Mizuta
authors.forename: Jun-ichi
authors.initials: J
authors.lastname: Banba
authors.forename: Takashi
authors.initials: T
authors.lastname: Kanamori
authors.forename: Ryuya
authors.initials: R
authors.lastname: Tawarada
authors.forename: Akihiro
authors.initials: A
authors.lastname: Ohkubo
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Sekine
authors.forename: Kohji
authors.initials: K
authors.lastname: Seio
mesh_terms: D004247:DNA / Q000737:chemistry*; D003841:Deoxycytidine / Q000031:analogs & derivatives* / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry*
chemical_list: D009841:Oligonucleotides; C051802:triplex DNA; D003841:Deoxycytidine; D004247:DNA