What are the applications of fluorescence quenching?

There are several applications of fluorescence quenching. One application includes its use as an indicator of DNA hybridization. In DNA hybridization, fluorophore and quencher molecules become attached to ends of ssDNA and close to one another, causing a loop. As DNA becomes hybridized and attaches to another ssDNA chain, the fluorophore-quencher complex is cleaved, allowing for the fluorophore to generate light. 

Another application involves the Forester mechanism of fluorescence quenching. This mechanism is used to determine the distance between acceptor and donor molecules, and is dependent on the intensity of quenching. This mechanism determines the conformation or size of a protein and also any protein-protein interactions.