Optimizing the SYBR green related cyanine dye structure to aim for brighter nucleic acid visualization

In recent years, the studies of RNA and its use for development based vaccines have increased drastically. Although cyanine dyes are commonly used probes studying nucleic acids, in a wide range applications, there is still growing need better brighter dyes. To meet this demand, we systematically studied structure SYBR green-related to gain deeper understanding their interactions with biomolecules especially how they interact acids structural components which makes them strongly fluorescent. Herein, five new were synthesized, photophysical properties evaluated. Observations characteristics compared calculations by using density functional theory ground state time-dependent form model optical absorption spectra excited selected molecules. Single crystal X-ray structures determined dye-DNA complex molecular docking dynamics calculations. Three features discovered: a) removing benzene ring from thiazolium moiety dye lowers fluorescence drastically, that quantum yield can be enhanced, therefore increasing fluorescence, b) incorporating methanethiol substituent at quinoline instead dimethylamine or c) changing an oxazolium moiety.