title: Recognition of triplex forming oligodeoxynucleotides incorporating abasic sites by 5-arylcytosine residues in duplex DNAs.
abstract: In this paper, we reported our attempt to use a 5arylcytosine (dC(ar)) and the abasic site () as an artificial base pair for DNA triplex. The idea was confirmed by the molecular modeling studied in which the aromatic group of (ph) which protrudes in the major groove was buried into the cleft formed by the residue in the TFO. We synthesized three kinds of dC(ar) and the oligonucleotides incorporating them. Our UV-melting experiments revealed that the DNA triplex containing the dC(ph).phi was more stable than that containing dC.phi pair. Moreover, the dC.phi pair was more stable than any other dC.Y pairs such as dC(ph).G, dC(ph).C, dC(ph).T and dC(ph).A. These results indicated the possibility that the appropriate pair of dC(Ar) and could be the new sequence code of DNA triplex. We also carried out the Tm analyses of other TFOs incorporating dC(Ar) and , and clarified the stability of these triplexes.
authors.affiliation: Department of life science, Tokyo Institute of Tecnology and CREST, JST, 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: 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: D020029:Base Pairing; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*
chemical_list: C528344:5-phenylcytosine; D009838:Oligodeoxyribonucleotides; C051802:triplex DNA; D003596:Cytosine; D004247:DNA