title: PRODAN-conjugated DNA: synthesis and photochemical properties.
abstract: A solvatochromic fluorophore, PRODAN, has been used as a microenvironment-sensitive reporter. Based on the chemistry of PRODAN, we designed and synthesized four novel fluorescent nucleosides, PDNX (X = U, C, A, and G), to which a PRODAN fluorophore was attached at pyrimidine C5 or purine C8. The fluorescent nucleosides sensitively varied the Stokes shift values depending on the orientational polarizability of the solvent. The PDNX incorporated into DNA also changed the Stokes shift values depending on the DNA structure. In particular, the excitation spectrum of the PDNX-containing duplex shifted to a longer wavelength and gave a smaller Stokes shift value when the base opposite PDNX could form a Watson-Crick base pair with PDNX. A lower energy excitation of PDNX-containing DNA resulted in a strong fluorescence emission selective to the Watson-Crick pairing base. This unique photochemical character was applicable to the efficient typing of single-nucleotide polymorphisms of genes.
authors: Frontier Research System, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-1098, Japan.
authors: Kazuki
authors: K
authors: Tainaka
authors: Kazuo
authors: K
authors: Tanaka
authors: Shuji
authors: S
authors: Ikeda
authors: Ken-ichiro
authors: K
authors: Nishiza
authors: Tomo
authors: T
authors: Unzai
authors: Yoshimasa
authors: Y
authors: Fujiwara
authors: Isao
authors: I
authors: Saito
authors: Akimitsu
authors: A
authors: Okamoto
mesh_terms: D015081:2-Naphthylamine / Q000031:analogs & derivatives* / Q000737:chemistry; D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry*; D005838:Genotype; D015394:Molecular Structure; D009705:Nucleosides / Q000737:chemistry; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D010777:Photochemistry; D012997:Solvents; D044366:Transition Temperature
chemical_list: D009705:Nucleosides; D009838:Oligodeoxyribonucleotides; D012997:Solvents; C038517:prodan; D004247:DNA; D015081:2-Naphthylamine