title: Light-up fluorescent probes utilizing binding behavior of perylenediimide derivatives to a hydrophobic pocket within DNA.
abstract: Here we study the binding behavior of perylenediimide () derivatives to a hydrophobic pocket created inside DNA and their photochemical properties capable of designing a light-up fluorescent sensor for short single-stranded DNA or RNA. The perylenediimide derivative with alkoxy groups () suppressing electron transfer quenching was examined. The bound randomly to DNA showed negligible fluorescence due to the aggregation-induced quenching, whereas the bound to the pocket as a monomeric form showed more than 100-fold fluorescence enhancement. Switching the binding states of the corresponded to a change in the fluorescence response for the hybridization event, which allowed us to design a fluorescent sensor of nucleic acids with a nanomolar detection limit.
authors.affiliation: Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan. takada@eng.u-hyogo.ac.jp yamana@eng.u-hyogo.ac.jp.
authors.forename: Tadao
authors.initials: T
authors.lastname: Takada
authors.forename: Kosato
authors.initials: K
authors.lastname: Yamaguchi
authors.forename: Suguru
authors.initials: S
authors.lastname: Tsukamoto
authors.forename: Mitsunobu
authors.initials: M
authors.lastname: Nakamura
authors.forename: Kazushige
authors.initials: K
authors.lastname: Yamana
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004277:DNA, Single-Stranded / Q000032:analysis*; D005456:Fluorescent Dyes / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D007094:Imides / Q000737:chemistry*; D009696:Nucleic Acids / Q000032:analysis; D010569:Perylene / Q000031:analogs & derivatives* / Q000737:chemistry; D012313:RNA / Q000032:analysis; D013050:Spectrometry, Fluorescence
chemical_list: D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes; D007094:Imides; D009696:Nucleic Acids; C521332:perylenediimide; D010569:Perylene; D012313:RNA