title: Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation.
abstract: We developed fluorescent turn-on probes containing a fluorescent nucleoside, 5-(benzofuran-2-yl)deoxyuridine (dU(BF)) or 5-(3-methylbenzofuran-2-yl)deoxyuridine (dU(MBF)), for the detection of single-stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU(MBF) achieved superior fluorescence enhancement than that containing dU(BF). NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3-methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3-methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex-induced fluorescence enhancement of the oligonucleotide probe containing dU(MBF).
authors.affiliation: Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501 (Japan).
authors.forename: Takashi
authors.initials: T
authors.lastname: Kanamori
authors.forename: Hiroki
authors.initials: H
authors.lastname: Ohzeki
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Masaki
authors.forename: Akihiro
authors.initials: A
authors.lastname: Ohkubo
authors.forename: Mari
authors.initials: M
authors.lastname: Takahashi
authors.forename: Kengo
authors.initials: K
authors.lastname: Tsuda
authors.forename: Takuhiro
authors.initials: T
authors.lastname: Ito
authors.forename: Mikako
authors.initials: M
authors.lastname: Shirouzu
authors.forename: Kanako
authors.initials: K
authors.lastname: Kuwasako
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Muto
authors.forename: Mitsuo
authors.initials: M
authors.lastname: Sekine
authors.forename: Kohji
authors.initials: K
authors.lastname: Seio
mesh_terms: D001483:Base Sequence; D001572:Benzofurans / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000737:chemistry; D003857:Deoxyuridine / Q000031:analogs & derivatives / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D014498:Uracil / Q000737:chemistry*
chemical_list: D001572:Benzofurans; D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes; D009841:Oligonucleotides; C051802:triplex DNA; D014498:Uracil; D012313:RNA; D004247:DNA; C105430:benzofuran; D003857:Deoxyuridine
keywords: DNA structures; NMR spectroscopy; RNA; fluorescent probes; sensors