Signal control by self-assembly of fluorophores in a molecular beacon-a model study

Pyrene excimer fluorescence is efficiently regulated through formation of pi-stacked aggregates between dialkynylpyrene (Y) and perylenediimide (E) residues located in the stem region of a molecular beacon (MB). The building blocks form organized, multichromophoric complexes in the native form. Hybridization to the target results in a conformational reorganization of the chromophores. The nature of the aggregates was investigated by changing the number of chromophores and natural base pairs in the beacon stem. The formation of different types of complexes (EYEY -> YEY -> EY) is revealed by characteristic spectroscopic changes. The data show that signal control is an intrinsic property of the interacting chromophores. The directed assembly of non-nucleosidic chromophores can be used for the generation of an on/ off switch of a fluorescence signal. The concept may find applications in various types of light-based input/ output systems.