Autofluorescence

Autofluorescence is the fluorescence of other substances than the fluorophore of interest. It increases the background signal.

Autofluorescence can be problematic in fluorescence microscopy. In most fluorescence microscopy, fluorescent stains (such as fluorescently-labeled antibodies) are applied to samples to stain specific structures. Autofluorescence interferes with detection of the resulting specific fluorescent signals, especially when the signals of interest are very dim — it causes structures other than those of interest to become visible. Depending upon the shape of the structures of interest and the other structures, it may not be obvious that this has occurred. In some microscopes (mainly confocal microscopes), it is possible to make use of different lifetime of the excited states of the added fluorescent markers and the endogenous molecules to exclude most of the autofluorescence.

In a few cases, autofluorescence may actually illuminate the structures of interest, or serve as a useful diagnostic indicator.

Biological autofluorescence: "Cells contain molecules, which become fluorescent when excited by UV/Vis radiation of suitable wavelength. This fluorescence emission, arising from endogenous fluorophores, is an intrinsic property of cells and is called auto-fluorescence to be distinguished from fluorescent signals obtained by adding exogenous markers. The majority of cell auto-fluorescence originates from mitochondria and lysosomes. Together with aromatic amino acids and lipo-pigments, the most important endogenous fluorophores are pyridinic (NADPH) and flavin coenzymes. In tissues, the extracellular matrix often contributes to the auto-fluorescence emission more than the cellular component, because collagen and elastin have, among the endogenous fluorophores, a relatively high quantum yield. Changes occurring in the cell and tissue state during physiological and/or pathological processes result in modifications of the amount and distribution of endogenous fluorophores and chemical-physical properties of their microenvironment. Therefore, analytical techniques based on auto-fluorescence monitoring can be utilized in order to obtain information about morphological and physiological state of cells and tissues. Moreover, auto-fluorescence analysis can be performed in real time because it does not require any treatment of fixing or staining of the specimens. In the past few years spectroscopic and imaging techniques have been developed for many different applications both in basic research and diagnostics." [Biotechnol Annu Rev. 2005;11:227-56. Cell and tissue autofluorescence research and diagnostic applications.Monici M.]

Examples
Without labelling, these substances show fluorescence. Because of scattering, it is better to use the nonlinear two photon excited fluorescence microscopy. melanin lipofuscin ceroid
 * chlorophyll (in plant cells)
 * collagen
 * elastin
 * fibrillin
 * flavin
 * indolamine
 * indolamine dimer
 * indolamine trimer
 * lipofuscin
 * NADH (reduced form only)
 * polyphenols (in plant cells)
 * tryptophan

自体荧光