title: DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes.
abstract: We have previously reported DNA triplexes containing the unnatural base triad G-PPI·C3, in which PPI is an indole-fused cytosine derivative incorporated into DNA duplexes and C3 is an abasic site in triplex-forming oligonucleotides (TFOs) introduced by a propylene linker. In this study, we developed a new unnatural base triad A-ψ·C(R1) where ψ and C(R1) are base moieties 2'-deoxypseudouridine and 5-substituted deoxycytidine, respectively. We examined several electron-withdrawing substituents for R1 and found that 5-bromocytosine (C(Br)) could selectively recognize ψ. In addition, we developed a new PPI derivative, PPI(Me), having a methyl group on the indole ring in order to achieve selective triplex formation between DNA duplexes incorporating various Watson-Crick base pairs, such as T-A, C-G, A-ψ, and G-PPI(Me), and TFOs containing T, C, C(Br), and C3. We studied the selective triplex formation between these duplexes and TFOs using UV-melting and gel mobility shift assays.
authors.forename: Takashi
authors.initials: T
authors.lastname: Kanamori
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Masaki
authors.forename: Masahiro
authors.initials: M
authors.lastname: Mizuta
authors.forename: Hirosuke
authors.initials: H
authors.lastname: Tsunoda
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: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009705:Nucleosides / Q000737:chemistry*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D009943:Organophosphorus Compounds / Q000737:chemistry
chemical_list: D009705:Nucleosides; D009838:Oligodeoxyribonucleotides; D009943:Organophosphorus Compounds; C434331:phosphoramidite; C051802:triplex DNA; D004247:DNA