Protein-Based Fluors

Two of the most commonly used fluorophores in flow cytometry, R-phycoerythrin (R-PE) and allophycocyanin (APC), are phycobiliproteins originally derived from algae. Both proteins contain fluorescent phycobilin chromophores embedded into a protein scaffolding which accounts for their large size. When phycobiliproteins are exposed to organic solvents like MeOH and EtOH, they denature and are no longer able to fluoresce. Both R-PE and APC are fairly bright fluors and are often used in flow cytometry to detect proteins with low levels of expression.

Another protein-based dye, PerCP, a peridinin-chlorophyll protein complex, is derived from photosynthetic dinoflagellates. Other fluorescent proteins, like eGFP, mCherry, and tdTomato can be fused to a protein of interest to visualize or track cell processes. These are typically derived from sea anemone and jellyfish, and exist as either monomers, dimers, or trimers. All of these protein-based dyes can be used as the donor molecule in FRET pairs. Generally, antibodies conjugated to protein-based flours are not commonly used in standard microscopy as they are more susceptible to photobleaching.