Development of novel PRODAN-labeled nucleosides as base-discriminating fluorescent probes.
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.
Tainaka
Kazuki
K
Frontier Research System, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
Ikeda
Shuji
S
Tanaka
Kazuo
K
Nishiza
Ken-ichiro
K
Fujiwara
Yoshimasa
Y
Okamoto
Akimitsu
A
Saito
Isao
I
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
D005456:Fluorescent Dyes; D015345:Oligonucleotide Probes; D011684:Purine Nucleosides; D011741:Pyrimidine Nucleosides; D015081:2-Naphthylamine