Alkynes fluorescence dyes

Mercury. A short account of the discovery of metal-catalyzed hydration of alkynes by Kucherov (1881) appeared on the occasion of its 125th anniversary [116]. Mercury-catalyzed hydration of alkynes has been used as mechanistic principle for devising fluorogenic probes for mercuric ions by two research teams. In one system, a 3-butyn-l-yl group at the phenolic oxygen of a fluorescein dye was cleaved via catalytic oxymercuration and elimination to releases a fluorescent dye (Scheme 20) [117]. In another system the mercury-catalyzed hydration of an ethynyl to an acetyl group provoked the quenching of fluorescence in a coumarine-based dye [118]. 

Generation of chemical patterns with photoreactive polymers photo-Diels-Alder surface anchoring followed by azide-alkyne click reaction to immobilize fluorescent dyes, (a) SPAAC strain-promoted azide-alkyne cycloaddition and (b) CuAAC Cu(l)-catalyzed azide-alkyne cycloaddition. (Source Adapted with permission from Reference [36d].)... 

Preparation of the future main chain occurred via activated PFP-ester chemistry, as discussed in Sect. 2. For this, PFPA was used as monomer in a RAFT polymerization. After removal of the thioester chain end by treatment with excess AIBN, the aminolysis using monoamine-functionalized fluorescent dye (Oregon Green Cadaverine) and prop-2-yn-l-amine and l-aminopropan-2-ol was conducted. Via an azide-alkyne 1,3-dipolar cycloaddition, an azide-capped cyclodextrin was attached onto the alkyne units along the main chain. As demonstrated in Scheme 10, the cyclodextrin moiety works as a supramolecular binding site for adamantyl residues. This supramolecular binding concept resulted ultimately in linear-g-(linear-hyperbranched) graft terpolymers. 

Several reports have been made using this reaction as a protein bioconjugation technique. In the first report, 60 azide functional groups attached to the surface of the cowpea mosaic virus (CPMV) using NHS ester or iodoacetamide reactions served as attachment sites for fluorescent alkyne derivatives [92]. The optimal conditions for the reaction were 21 pM protein (based on azide-functionalized capsid monomers), 1 mM CuS04, 2 mM TCEP, and 2 mM 58 in pH 8 buffer at 4°C for 16 h. As an alternative, small amounts of copper wire were also effective in generating and maintaining the Cu(I) species. The reaction was also successful when the alkynes were attached to the viral capsid and azides were attached to the dye. 

The C5 position of dU has been used to attach a variety of labels or reporter groups, in particular fluorophores ° (see section 3.5). The pyrene-modified analogue (39) has been used to detect RNA bulge conformations in the HIV-TAR RNA sequence where the fluorescence is greatly enhanced,and as a donor for the red emitter nile red (40) when the two dyes are adjacent in duplex DNA the result is white light that is emitted upon excitation of (39). A zinc-porphyrin complex has been added to C5 of dU for use in electron transfer. Norbornene has been attached via an alkyne linker for post-synthetic modification with nitrile oxides in a copper-free Click reaction, " and various dienes have been attached for Diels-Alder tagging of DNA. The photoaffinity tag (41) has been incorporated into DNA adjacent to a damaged DNA base (8-oxo-dG or thymine dimer) such that when exposed to repair systems, the repair enzyme is trapped by the diazirine for mass spectroscopic characterisation. ... 

This breadth of reactivity necessitates understanding and control of selectivity. To this end, Sohn and Ihee have conducted fluorescence resonance energy transfer experiments with a range of catalysts, with specially designed alkenes, allenes, and alkynes that are tethered to a dye (Figure 2.12). When the ruthenium complex coordinates the alkene/allene/alkyne, the fluorescence is quenched. Catalysts studied included Mol, Gl, G2, GHl, and GH2 rate constants and thermodynamic parameters were obtained in each case (Table 2.8). These experiments showed that catalyst systems react... 

Fig. 6 Left Cell-selective BONCAT method. Cells that cany the mmant MetRS (NLL-MRS) can be labeled with the methionine surrogate azidonorleucine (Anl, 2). Other cells are inert to Anl. Right Bacterial cells carrying the NLL synthetase are labeled with a fluorescent alkyne dye (green) in the presence of mammalian macrophages (red). Maraophage proteins are not labeled...

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