Autofluorescence is the light naturally emitted by biological structures such as mitochondria and lysosomes when they absorb light, and is used to distinguish light originating from artificially added fluorescent labels (fluorophores).
The most common autofluorescent molecules are NADPH and flavin; the extracellular matrix can also contribute to autofluorescence because of the intrinsic properties of collagen and elastin.
Typically, proteins containing increased amounts of the amino acids tryptophan, tyrosine and phenylalanine show some degree of autofluorescence.
In medicine, there is the use of electric radiation to induce autofluorescence in the human body to diagnose diseases such as cancer.
Autofluorescence can be problematic in fluorescence microscopy. Luminescent dyes, such as fluorescently labeled antibodies, are applied to the sample to make specific structures visible.
Autofluorescence interferes with the detection of specific fluorescent signals, especially when the signal of interest is very dim – it makes structures other than the structure of interest visible.
In some microscopes (mainly confocal microscopes) added fluorescent labels and different lifetimes of the excited states of endogenous molecules can be exploited to rule out most autofluorescence.
In a few cases, autofluorescence can actually illuminate structures of interest, or serve as useful diagnostic indicators.
You may be interested in the following fluorophore dye:
APDye 488 Maleimide ( Alexa fluor 488 maleimide equivalent )