title: Development of novel PRODAN-labeled nucleosides as base-discriminating fluorescent probes.
abstract: We have developed a PRODAN-labeled uridine ((PDN)U), which contains a polarity-sensitive chromophore at the C-5 position of uracil. This paper describes the synthesis and fluorescent properties of oligodeoxy-nucleotides (ODNs) containing PRODAN-labeled nucleosides ((PDN)C, (PDN)A, and (PDN)G). PRODAN chromophore was attached to cytosine at the C-5 position and to purine bases at the C-8 position to extend into the major groove. When BDF probes containing a PRODAN-labeled nucleoside hybridize with a "full-matched" ODN, the fluorescence spectrum showed a strong emission around 520 nm on 450 nm excitation. In contrast, when PRODAN-labeled nucleoside analogs form a "mismatched" base pair, the fluorescence was weaker.
authors.affiliation: Frontier Research System, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Tainaka
authors.forename: Shuji
authors.initials: S
authors.lastname: Ikeda
authors.forename: Kazuo
authors.initials: K
authors.lastname: Tanaka
authors.forename: Ken-ichiro
authors.initials: K
authors.lastname: Nishiza
authors.forename: Yoshimasa
authors.initials: Y
authors.lastname: Fujiwara
authors.forename: Akimitsu
authors.initials: A
authors.lastname: Okamoto
authors.forename: Isao
authors.initials: I
authors.lastname: Saito
mesh_terms: D015081:2-Naphthylamine / Q000031:analogs & derivatives* / Q000138:chemical synthesis / Q000737:chemistry; D005456:Fluorescent Dyes / Q000138:chemical synthesis / Q000737:chemistry*; D015345:Oligonucleotide Probes / Q000737:chemistry*; D020641:Polymorphism, Single Nucleotide; D011684:Purine Nucleosides / Q000138:chemical synthesis / Q000737:chemistry*; D011741:Pyrimidine Nucleosides / Q000138:chemical synthesis / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D011684:Purine Nucleosides; D011741:Pyrimidine Nucleosides; D015081:2-Naphthylamine