Genetically Encoded\nFluorogenic DNA Aptamers for Imaging\nMetabolite in Living Cells

Genetically encoded fluorescent protein\nand fluorogenic\nRNA sensors\nare indispensable tools for imaging biomolecules in cells. To expand\nthe toolboxes and improve the generalizability and stability of this\ntype of sensor, we report herein a genetically encoded fluorogenic\nDNA aptamer (GEFDA) sensor by linking a fluorogenic DNA aptamer for\ndimethylindole red with an ATP aptamer. The design enhances red fluorescence\nby 4-fold at 650 nm in the presence of ATP. Additionally, upon dimerization,\nit improves the signal-to-noise ratio by 2–3 folds. We further\nintegrated the design into a plasmid to create a GEFDA sensor for\nsensing ATP in live bacterial and mammalian cells. This work expanded\ngenetically encoded sensors by employing fluorogenic DNA aptamers,\nwhich offer enhanced stability over fluorogenic proteins and RNAs,\nproviding a novel tool for real-time monitoring of an even broader\nrange of small molecular metabolites in biological systems.