title: Cytosine detection by a fluorescein-labeled probe containing base-discriminating fluorescent nucleobase.
abstract: We report on a new method for the detection of a base at a specific site in a DNA sequence by monitoring the fluorescence emission of fluorescein. To achieve this goal, we developed a new base-discriminating fluorescent (BDF) nucleobase, naphthodeazaadenine ((ND)A). The fluorescence spectrum of the duplex possessing a cytosine base as a complementary base of (ND)A showed a fluorescence peak at 383 nm when using an excitation wavelength of 350 nm. When the complementary base of (ND)A was one of the other bases, the fluorescence intensity was very low. The fluorescence emission spectrum of (ND)A overlapped with the fluorescence excitation spectrum of fluorescein in the wavelength range of 400-500 nm. Thus, we designed FRET-BDF probes containing (ND)A as the FRET donor and fluorescein as the acceptor. The interaction of these two fluorophores, which are separated by defined base pairs, allowed an efficient energy transfer that resulted in a dominant fluorescence emission of fluorescein at 520 nm when using an excitation wavelength of 350 nm. Fluorescence emission from FRET-BDF probes was observed only when the complementary base of (ND)A is C, thus achieving a clear distinction of a C base on the complementary DNA strand. However, the general utility of our method is limited due to the quenching of the (ND)A fluorescence by a G/C base pair flanking (ND)A.
authors.affiliation: Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University and SORST, Japan Science and Technology Corporation, Kyoto 615-8510, Japan.
authors.forename: Akimitsu
authors.initials: A
authors.lastname: Okamoto
authors.forename: Kazuo
authors.initials: K
authors.lastname: Tanaka
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Fukuta
authors.forename: Isao
authors.initials: I
authors.lastname: Saito
mesh_terms: D020029:Base Pairing; D003596:Cytosine / Q000032:analysis*; D015342:DNA Probes / Q000737:chemistry; D004735:Energy Transfer; D019793:Fluorescein; D005456:Fluorescent Dyes / Q000737:chemistry; D007202:Indicators and Reagents; D013050:Spectrometry, Fluorescence
chemical_list: D015342:DNA Probes; D005456:Fluorescent Dyes; D007202:Indicators and Reagents; D003596:Cytosine; D019793:Fluorescein