Development of natural product derivatives for the fluorimetric DNA detection in cells

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The staining of nucleic acids with organic dyes is an essential element of the fluorimetric analysis of cells and requires high standards of the employed materials and methods, so that there is still a great need for novel fluorophores. Hence, the low water-solubility and the limited cell permeability of synthetic fluorescent probes often limit their applicability and have to be overcome. In this project, it will be investigated whether fluorescent probes, that are derived from natural products, exhibit an improved biocompatibility as provided by their biogenic origin. Based on the results of our previous studies, derivatives of natural products shall be identified that are related to the quinolizinium ion, such as berberine or sempervirine, and that have resembling emission properties as the annelated quinolizinium fluorophore. By means of systematic structure variations, a series of derivatives will be made available whose photophysical properties and suitability as DNA-sensitive fluorescent probes will be examined in detail with spectroscopic methods and with confocal and high-resolution fluorescence microscopy. Specifically, those factors will be assessed that govern a strong and selective association of the substrates with the nucleic acid, along with a significant change of the emission properties of the bound ligand, thus enabling the unambiguous and sensitive detection. Furthermore, it will be examined whether the combination of the special photophysical and DNA-binding properties of the targeted fluorescent probes may also be employed for the characterization of the direct chemical environment of the DNA binding site, once an additional medium-sensitive substituent is introduced. For that purpose, hydroxy-substituted ligands will be identified that undergo an efficient and fluorimetrically detectable proton transfer in the excited state. Such strong photoacids are proposed to be well suited for the direct monitoring and characterization of the immediate chemical vicinity of the DNA-bound ligand by means of fluorimetric monitoring of the intermolecular proton transfer reaction with the surrounding medium. The resulting data will be used for the first time for the spatial- and time-resolved fluorimetric determination of the mobility and concentration of free or bound water molecules in the hydration shell of the DNA, either in gel- or hydrogel-type model systems or in cells.