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Fluorene-based fluorescent markers : new insights in synthesis and applications into labeling of nucleic acids and imaging of cell membranes

Abstract : Extensive research focuses on finding straightforward synthesis and prospective probes for biological applications. Push-pull dyes are of particular interest for various uses as biosensors for membranes and nucleic acids. These dyes are highly responsive to changes of their environments. Specifically, push-pull fluorenes exhibit low cytotoxicity and high photostability, but are not yet reported in the two mentioned applications. Furthermore, their synthesis is highly demanding. In this context, our work presents: 1) Step-economic and concise approaches to access challenging aminoaromatics via optimized air-stable Pd catalytic systems involving selective mono/di-amination and sequential one-pot synthesis, 2) Synthesis of a fluorene library varying the acceptor and the donor groups, 3) Structure-photophysics relationships, 4) Synthesis of three advanced dyes and concluding the first plasma membrane-specific fluorene probe that can be a powerful tool for studying the structure and biophysical dynamics of membranes. The optimal dye surpasses the features of commonly used probes showing: red-shifted absorption matching the 405 nm diode laser, higher brightness decreasing the dye concentration for staining by ~10-15 folds, high photostability, comparably strong sensitivity to liquid domains of cell membrane, and 5) Synthesis of 4 fluorene-labeled phosphoramidites and their site-specific ODN incorporations evidencing high sensitivity to protic media and pH. Labeled sequences exhibited a far-red emission with modest quantum yields in line with their strong charge transfer character. In DNA duplexes, the dye efficiently base-discriminated opposite cytidine and thymidine. A preliminary application of the DNA fluorescent marker involved testing it as a mega-Stokes shift donor in an emissive FRET pair in combination with Dy681 acceptor. The FRET demonstrated a ratiometric turn-on in NIR region with a shift of 300 nm
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Janah Shaya. Fluorene-based fluorescent markers : new insights in synthesis and applications into labeling of nucleic acids and imaging of cell membranes. Other. Université Côte d'Azur, 2016. English. ⟨NNT : 2016AZUR4066⟩. ⟨tel-02003596⟩

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