title: Development of a series of near-infrared dark quenchers based on Si-rhodamines and their application to fluorescent probes.
abstract: Near-infrared (NIR) fluorescent probes based on the Förster resonance energy transfer (FRET) mechanism have various practical advantages, and their molecular design is generally based on the use of NIR dark quenchers, which are nonfluorescent dyes, as cleavable FRET acceptors. However, few NIR dark quenchers can quench fluorescence in the Cy7 region (over 780 nm). Here, we describe Si-rhodamine-based NIR dark quenchers (SiNQs), which show broad absorption covering this region. They are nonfluorescent independently of solvent polarity and pH, probably due to free rotation of the bond between the N atom and the xanthene moiety. SiNQs can easily be structurally modified to tune their water-solubility and absorption spectra, enabling flexible design of appropriate FRET pair for various NIR fluorescent dyes. To demonstrate the usefulness of SiNQs, we designed and synthesized a NIR fluorescent probe for matrix metalloproteinase (MMP) activity using SiNQ780. This probe 1 could detect MMP activity in vitro, in cultured cells and in a tumor-bearing mouse, in which the tumor was clearly visualized, by NIR fluorescence. We believe SiNQs will be useful for the development of a wide range of practical NIR fluorescent probes.
authors.affiliation: †Graduate School of Pharmaceutical Sciences, ‡Open Innovation Center for Drug Discovery, and §Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.|¶PRESTO and ⊥CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
authors.forename: Takuya
authors.initials: T
authors.lastname: Myochin
authors.affiliation: †Graduate School of Pharmaceutical Sciences, ‡Open Innovation Center for Drug Discovery, and §Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.|¶PRESTO and ⊥CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
authors.forename: Kenjiro
authors.initials: K
authors.lastname: Hanaoka
authors.affiliation: †Graduate School of Pharmaceutical Sciences, ‡Open Innovation Center for Drug Discovery, and §Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.|¶PRESTO and ⊥CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
authors.forename: Shimpei
authors.initials: S
authors.lastname: Iwaki
authors.affiliation: †Graduate School of Pharmaceutical Sciences, ‡Open Innovation Center for Drug Discovery, and §Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.|¶PRESTO and ⊥CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
authors.forename: Tasuku
authors.initials: T
authors.lastname: Ueno
authors.affiliation: †Graduate School of Pharmaceutical Sciences, ‡Open Innovation Center for Drug Discovery, and §Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.|¶PRESTO and ⊥CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
authors.forename: Toru
authors.initials: T
authors.lastname: Komatsu
authors.affiliation: †Graduate School of Pharmaceutical Sciences, ‡Open Innovation Center for Drug Discovery, and §Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.|¶PRESTO and ⊥CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
authors.forename: Takuya
authors.initials: T
authors.lastname: Terai
authors.affiliation: †Graduate School of Pharmaceutical Sciences, ‡Open Innovation Center for Drug Discovery, and §Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.|¶PRESTO and ⊥CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Nagano
authors.affiliation: †Graduate School of Pharmaceutical Sciences, ‡Open Innovation Center for Drug Discovery, and §Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.|¶PRESTO and ⊥CREST, Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
authors.forename: Yasuteru
authors.initials: Y
authors.lastname: Urano
mesh_terms: D000818:Animals; D045744:Cell Line, Tumor; D002470:Cell Survival; D003624:Darkness; D015195:Drug Design; D004355:Drug Stability; D005456:Fluorescent Dyes / Q000737:chemistry*; D006801:Humans; D007259:Infrared Rays; D051379:Mice; D061848:Optical Imaging; D012235:Rhodamines / Q000737:chemistry*; D012825:Silicon / Q000737:chemistry*; D012995:Solubility; D014867:Water / Q000737:chemistry
chemical_list: D005456:Fluorescent Dyes; D012235:Rhodamines; D014867:Water; D012825:Silicon