Development of new fluorescent probes for nucleic acids based on aminophthalimide as isosteric base substitution and photostable cyanine-styryl dyes

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Fluorescent labeling plays not only a major role in chemical bioanalytics and molecular diagnostics, but also in the actually strongly expanding research field of molecular imaging of living cells. The central goal of this project remains to be the development of new fluorescent probes for nucleic acids, which are suitable for chemical biology based on their optimized structure and optical properties, and can replace weaker, but commercially available fluorescent probes. The focus of this project in the first funding period was the development of new fluorescent probes for DNA based on aminophthalimide that is isosteric to purines, and photostable cyanine-styryl dyes as postsynthetic modifications for DNA, as described in the project report and documented by publications. During the second funding period we propose to shift the focus onto RNA and develop these fluorescent probes for RNA. The particular challenges are still divided into two subprojects: (A) Isosteric probes with fluorophores that have approximately the small size of DNA/RNA bases but nonetheless show large Stokes’ shifts and applicable quantum yields are important because they do only slightly alter the structure of nucleic acids and their biological interactions (subproject A). In the first funding period, we established aminophthalimide as base surrogate for DNA. It should now be developed and established as RNA probe. (B) For the bioorthogonally and “clickable” fluorescent probes not only photostability is important for the application in long-lasting cellular imaging by single molecule spectroscopy, but also fluorogenic properties are determing these applications. The latter will be a new criterium for the second funding period. Fluorogenic probes have the great advantage that only those fluorophores are lighting up by their enhanced emission which are conjugated to RNA (and DNA) (subproject B). Taken together, this project will deliver new and powerful fluorescent probes for RNA bioanalytics and imaging.