What are tandem dyes in flow cytometry?

Tandem dyes refer to compounds in which two different fluorophores have been covalently linked. One of the fluorophores serves as donor and the other as acceptor, forming a fluorescence-resonance energy transfer (FRET) pair. Such a FRET pair behaves as a unique dye that has the excitation properties of the donor molecule and the emission properties of an acceptor molecule.

A donor molecule is generally either a protein-based dye [e.g. Phycoerythrin (PE) and Allophycocyanin (APC) ] or a chemically synthesized dye with a large extinction coefficient. An acceptor molecule is a synthetic dye which can form an effective FRET pair with the donor [e.g. Cyanine-5 (Cy5), Cyanine-5.5 (Cy5.5) and Cyanine-7 (Cy7)]. Examples of tandem dyes include PE-Cy7, PE-Cy5.5, APC-Cy5.5, and APC-Cy7.