Can cyanine dyes be used in tandem with other dyes?

Yes, cyanine dyes can be used in tandem with other dyes, resulting in what is more commonly known as ‘tandem dyes’. A tandem dye is made up of two covalently linked fluorescent molecules or fluorophores.  One fluorophore acts as the donor and the other acts as an acceptor.

A donor molecule could be either a protein-based dye such as Phycoerythrin (PE) or Allophycocyanin (APC), or it could be a chemically synthesized dye with a large extinction coefficient.

An acceptor molecule is generally a synthetic dye that absorbs energy emitted by the donor molecule, forming an effective FRET pair with the donor. Cy5 and Cy7 are the most well-known acceptor molecules. Examples of cyanine-based tandem dyes include PE-Cy5.5, APC-Cy5.5, PE-Cy7, and APC-Cy7.