Optimizing triangulenium dyes for biological applications:Live cell DNA binding and water-solubility

Fluorescent dyes are an important analytical tool. They see widespread use in biological sciences, where they help visualize anything from the dynamics of a cell to the localization of tumor tissue in patients. How the signal of a fluorophore is used can roughly be broken down into intensity-based measurements and lifetime-based measurements. In intensity-based methods, simply, the number of photons emitted by the fluorescent is recorded. In lifetime-based methods, the delay from excitation of a fluorescent dye till emission is used to gain information about the environment in which the dye is located. In this work a series of fluorescent dyes with exceptionally long fluorescence lifetimes are optimized for applications in biological sciences. Recent reports show that the fluorescent probe DAOTA-M2 gives a selective fluorescence lifetime response when bound to G-quadruplex DNA. It was investigated through analogues of the probe, what causes the selectivity over other DNA topologies. Quenching by photoinduced electron transfer from the appended morpholino-groups was found to be an important factor. From these findings a new series of morholino-substituted DAOTA+ dyes was synthesized to improve the fluorescence response in DNA binding. The large cationic triangulenium dyes are poorly soluble in water. Yet, the most interesting targets for their application are found in biological sciences, where water is almost always the solvent. Three strategies for making the DAOTA+ chromophore water-soluble were followed to synthesize the first water-soluble triangulenium dyes. Excellent photophysical properties werefound in aqueous solution of the new dyes. Based on the findings of the water-solubility study, a water-soluble long fluorescence lifetime triangulenium label for bioconjugation was prepared. The fluorescent label is expected to beuseful in the analysis of protein interactions.Lastly, it was investigated how triangulenium dyes could be synthesized to be more redshifted