Peroxynitrite-selective tools and their mechanism of detection. (A) Structure and mechanism of the small molecule FRET probe MITO-CC. The probe consists of a FRET donor and an acceptor as well as a linker, which is also the group responsible for sending the probe into mitochondria. In the absence of ONOO−, the probe emits at 650 nm due to energy transfer from the donor to the acceptor. However, upon reaction with ONOO−, the FRET acceptor is eliminated and decomposed, and the remaining donor fluoresces at 450 nm. (B) GFP variants sfGFP(66Thy) and pnGFP-Ultra with non-natural amino acids. Genetic code expansions on GFP using non-natural amino acids (shown in the boxes) led to the generation of GFPs that are non-fluorescent. The non-natural amino acids are equipped with ONOO− sensitive groups, which upon reaction are cleaved off and the resulting GFP is then fluorescent.