A fluorophore (or fluorochrome, similarly to a chromophore) is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with several π bonds.
Fluorophores are sometimes used alone, as a tracer in fluids, as a dye for staining of certain structures, as a substrate of enzymes, or as a probe or indicator (when its fluorescence is affected by environmental aspects such as polarity or ions). More generally they are covalently bonded to a macromolecule, serving as a marker (or dye, or tag, or reporter) for affine or bioactive reagents (antibodies, peptides, nucleic acids). Fluorophores are notably used to stain tissues, cells, or materials in a variety of analytical methods, i.e., fluorescent imaging and spectroscopy.
Fluorescein, by its amine reactive isothiocyanate derivative fluorescein isothiocyanate, has been one of the most popular fluorophores. From antibody labeling, the applications have spread to nucleic acids thanks to (FAM (Carboxyfluorescein), TET,...). Other historically common fluorophores are derivatives of rhodamine (TRITC), coumarin, and cyanine. Newer generations of fluorophores, many of which are proprietary, often perform better, being more photostable, brighter, and/or less pH-sensitive than traditional dyes with comparable excitation and emission.
The fluorophore absorbs light energy of a specific wavelength and re-emits light at a longer wavelength. The absorbed wavelengths, energy transfer efficiency, and time before emission depend on both the fluorophore structure and its chemical environment, as the molecule in its excited state interacts with surrounding molecules. Wavelengths of maximum absorption (≈ excitation) and emission (for example, Absorption/Emission = 485 nm/517 nm) are the typical terms used to refer to a given fluorophore, but the whole spectrum may be important to consider. The excitation wavelength spectrum may be a very narrow or broader band, or it may be all beyond a cutoff level. The emission spectrum is usually sharper than the excitation spectrum, and it is of a longer wavelength and correspondingly lower energy. Excitation energies range from ultraviolet through the visible spectrum, and emission energies may continue from visible light into the near infrared region.
Main characteristics of fluorophores are:
- Maximum excitation and emission wavelength (expressed in nanometers (nm)): corresponds to the peak in the excitation and emission spectra (usually one peak each),
- Molar absorption Coefficient ( in Molar−1cm−1): links the quantity of absorbed light, at a given wavelength, to the concentration of fluorophore in solution.
- Quantum yield: efficiency of the energy transferred from incident light to emitted fluorescence (= number of emitted photons per absorbed photons)
- Lifetime (in picoseconds): duration of the excited state of a fluorophore before returning to its ground state. It refers to the time taken for a population of excited fluorophores to decay to 1/e (≈0.368) of the original amount.
- Stokes shift: difference between the maximum excitation and maximum emission wavelengths.
These characteristics drive other properties, including the photobleaching or photoresistance (loss of fluorescence upon continuous light excitation). Other parameters should be considered, as the polarity of the fluorophore molecule, the fluorophore size and shape (i.e. for polarization fluorescence pattern), and other factors can change the behavior of fluorophores.
See more on fluorescence principle.
Size (molecular weight)
Most fluorophores are organic small molecules of 20 - 100 atoms (200 - 1000 Dalton - the molecular weight may be higher depending on grafted modifications, and conjugated molecules), but there are also much larger natural fluorophores that are proteins: Green fluorescent protein (GFP) is 27 kDa and several phycobiliproteins (PE, APC...) are ≈240kDa.
Fluorescence particles are not considered fluorophores (quantum dot: 2-10 nm diameter, 100-100,000 atoms).
The size of the fluorophore might sterically hinder the tagged molecule, and affect the fluorescence polarity.
Fluorophore molecules could be either utilized alone, or serve as a fluorescent motif of a functional system. Based on molecular complexity and synthetic methods, fluorophore molecules could be generally classified into four categories: proteins and peptides, small organic compounds, synthetic oligomers and polymers, and multi-component systems. 
Fluorescent proteins GFP (green), YFP (yellow) and RFP (red) can be attached to other specific proteins to form a fusion protein, synthesized in cells after transfection of a suitable plasmid carrier.
Non-protein organic fluorophores belong to following major chemical families:
- Xanthene derivatives: fluorescein, rhodamine, Oregon green, eosin, and Texas red
- Cyanine derivatives: cyanine, indocarbocyanine, oxacarbocyanine, thiacarbocyanine, and merocyanine
- Squaraine derivatives and ring-substituted squaraines, including Seta and Square dyes
- Squaraine Rotaxane derivatives: SeTau dyes
- Naphthalene derivatives (dansyl and prodan derivatives)
- Coumarin derivatives
- oxadiazole derivatives: pyridyloxazole, nitrobenzoxadiazole and benzoxadiazole
- Anthracene derivatives: anthraquinones, including DRAQ5, DRAQ7 and CyTRAK Orange
- Pyrene derivatives: cascade blue, etc.
- Oxazine derivatives: Nile red, Nile blue, cresyl violet, oxazine 170, etc.
- Acridine derivatives: proflavin, acridine orange, acridine yellow, etc.
- Arylmethine derivatives: auramine, crystal violet, malachite green
- Tetrapyrrole derivatives: porphin, phthalocyanine, bilirubin
These fluorophores fluoresce due to delocalized electrons which can jump a band and stabilize the energy absorbed. Benzene, one of the simplest aromatic hydrocarbons, for example, is excited at 254 nm and emits at 300 nm. This discriminates fluorophores from quantum dots, which are fluorescent semiconductor nanoparticles.
They can be attached to protein to specific functional groups, such as - amino groups (Active ester, Carboxylate, Isothiocyanate, hydrazine) - carboxyl groups (carbodiimide) - thiol (maleimide, acetyl bromide) - azide (via click chemistry or non-specifically (glutaraldehyde)).
Additionally, various functional groups can be present to alter its properties, such as solubility, or confer special properties, such as boronic acid which binds to sugars or multiple carboxyl groups to bind to certain cations. When the dye contains an electron-donating and an electron-accepting group at opposite ends of the aromatic system, this dye will probably be sensitive to the environment's polarity (solvatochromic), hence called environment-sensitive. Often dyes are used inside cells, which are impermeable to charged molecules, as a result of this the carboxyl groups are converted into an ester, which is removed by esterases inside the cells, e.g., fura-2AM and fluorescein-diacetate.
The following dye families are trademark groups, and do not necessarily share structural similarities.
- CF dye (Biotium)
- DRAQ and CyTRAK probes (BioStatus)
- BODIPY (Invitrogen)
- EverFluor (Setareh Biotech)
- Alexa Fluor (Invitrogen)
- Bella Fluor (Setareh Biotech)
- DyLight Fluor (Thermo Scientific, Pierce)
- Atto and Tracy (Sigma Aldrich)
- FluoProbes (Interchim)
- Abberior Dyes (Abberior)
- DY and MegaStokes Dyes (Dyomics)
- Sulfo Cy dyes (Cyandye)
- HiLyte Fluor (AnaSpec)
- Seta, SeTau and Square Dyes (SETA BioMedicals)
- Quasar and Cal Fluor dyes (Biosearch Technologies)
- SureLight Dyes (APC, RPEPerCP, Phycobilisomes)(Columbia Biosciences)
- APC, APCXL, RPE, BPE (Phyco-Biotech, Greensea, Prozyme, Flogen)
- Vio Dyes (Miltenyi Biotec)
Examples of frequently encountered fluorophores
Reactive and conjugated dyes
|Dye||Ex (nm)||Em (nm)||MW||Notes|
|R-Phycoerythrin (PE)||480;565||578||240 k|
|PE-Cy5 conjugates||480;565;650||670||aka Cychrome, R670, Tri-Color, Quantum Red|
|Red 613||480;565||613||PE-Texas Red|
|PerCP||490||675||35kDa||Peridinin chlorophyll protein|
|Fluorescein||495||519||389||FITC; pH sensitive|
|G-Dye100||498||524||suitable for protein labeling and electrophoresis|
|G-Dye200||554||575||suitable for protein labeling and electrophoresis|
|G-Dye300||648||663||suitable for protein labeling and electrophoresis|
|G-Dye400||736||760||suitable for protein labeling and electrophoresis|
|Lissamine Rhodamine B||570||590|
|Texas Red||589||615||625||Sulfonyl chloride|
|Allophycocyanin (APC)||650||660||104 k|
|APC-Cy7 conjugates||650;755||767||Far Red|
Nucleic acid dyes
|Dye||Ex (nm)||Em (nm)||MW||Notes|
|Ethidium Bromide||210;285||605||394||in aqueous solution|
|TOTO-1, TO-PRO-1||509||533||Vital stain, TOTO: Cyanine Dimer|
|TO-PRO: Cyanine Monomer|
|CyTRAK Orange||520||615||-||(Biostatus) (red excitation dark)|
|Propidium Iodide (PI)||536||617||668.4|
|LDS 751||543;590||712;607||472||DNA (543ex/712em), RNA (590ex/607em)|
|7-AAD||546||647||7-aminoactinomycin D, CG-selective|
|DRAQ5||600/647||697||413||(Biostatus) (usable excitation down to 488)|
|DRAQ7||599/644||694||~700||(Biostatus) (usable excitation down to 488)|
Cell function dyes
|Dye||Ex (nm)||Em (nm)||MW||Notes|
|Indo-1||361/330||490/405||1010||AM ester, low/high calcium (Ca2+)|
|Fluo-3||506||526||855||AM ester. pH > 6|
|Fluo-4||491/494||516||1097||AM ester. pH 7.2|
|DCFH||505||535||529||2'7'Dichorodihydrofluorescein, oxidized form|
|DHR||505||534||346||Dihydrorhodamine 123, oxidized form, light catalyzes oxidation|
|Dye||Ex (nm)||Em (nm)||MW||QY||BR||PS||Notes|
|GFP (Y66H mutation)||360||442|
|GFP (Y66F mutation)||360||508|
|GFP (Y66W mutation)||436||485|
|GFP (S65A mutation)||471||504|
|Midoriishi Cyan||472||495||0.9||25||dimer (MBL)|
|Wild Type GFP||396,475||508||26k||0.77|
|GFP (S65C mutation)||479||507|
|TurboGFP||482||502||26 k||0.53||37||dimer, (Evrogen)|
|GFP (S65L mutation)||484||510|
|Emerald||487||509||0.68||39||0.69||weak dimer, (Invitrogen)|
|GFP (S65T mutation)||488||511|
|EGFP||488||507||26k||0.60||34||174||weak dimer, (Clontech)|
|Azami Green||492||505||0.74||41||monomer (MBL)|
|EYFP||514||527||26k||0.61||51||60||weak dimer, (Clontech)|
|TurboYFP||525||538||26 k||0.53||55.7||dimer, (Evrogen)|
|Kusabira Orange||548||559||0.60||31||monomer (MBL)|
|Allophycocyanin (APC)||652||657.5||105 kDa||0.68||heterodimer, crosslinked|
|TurboRFP||553||574||26 k||0.67||62||dimer, (Evrogen)|
|DsRed monomer||556||586||~28k||0.1||3.5||16||monomer, (Clontech)|
|TurboFP602||574||602||26 k||0.35||26||dimer, (Evrogen)|
|mRFP1||584||607||~30k||0.25||monomer, (Tsien lab)|
|R-phycoerythrin (RPE)||565 >498||573||250 kDa||0.84||heterotrimer|
|B-phycoerythrin (BPE)||545||572||240 kDa||0.98||heterotrimer|
|P3||614||662||~10,000 kDa||phycobilisome complex|
|Peridinin Chlorophyll (PerCP)||483||676||35 kDa||trimer|
|mKate (TagFP635)||588||635||15||monomer (Evrogen)|
|TurboFP635||588||635||26 k||0.34||22||dimer, (Evrogen)|
|mRaspberry||598||625||0.15||13||monomer, faster photobleach than mPlum|
Ex (nm): Excitation wavelength in nanometers
Em (nm): Emission wavelength in nanometers
MW: Molecular weight
QY: Quantum yield
BR: Brightness: Molar absorption coefficient * quantum yield / 1000
PS: Photostability: time [sec] to reduce brightness by 50%
Fluorophores have particular importance in the field of biochemistry and protein studies, e.g., in immunofluorescence but also in cell analysis, e.g. immunohistochemistry  and small molecule sensors.
Uses outside the life sciences
Additionally fluorescent dyes find a wide use in industry, going under the name of "neon colours", such as
- multi-ton scale usages in textile dyeing and optical brighteners in laundry detergents
- advanced cosmetic formulations; safety equipment and clothing
- organic light-emitting diodes (OLED)
- fine arts and design (posters and paintings)
- synergists for insecticides and experimental drugs
- used as a dye in highlighters to give off a glow-like effect
- solar panels (collect more light / wavelengths)
- Category:Fluorescent dyes
- Fluorescence in the life sciences
- Dark quencher
- Fluorescence recovery after photobleaching (FRAP) - an application for quantifying mobility of molecules in lipid bilayers.
- Juan Carlos Stockert, Alfonso Blázquez-Castro (2017). "Chapter 3 Dyes and Fluorochromes". Fluorescence Microscopy in Life Sciences. Bentham Science Publishers. pp. 61–95. ISBN 978-1-68108-519-7. Retrieved 24 December 2017.
- Rietdorf J (2005). Microscopic Techniques. Advances in Biochemical Engineering / Biotechnology. Berlin: Springer. pp. 246–9. ISBN 3-540-23698-8. Retrieved 2008-12-13.
- Tsien RY; Waggoner A (1995). "Fluorophores for confocal microscopy". In Pawley JB (ed.). Handbook of biological confocal microscopy. New York: Plenum Press. pp. 267–74. ISBN 0-306-44826-2. Retrieved 2008-12-13.
- Lakowicz, JR (2006). Principles of fluorescence spectroscopy (3rd ed.). Springer. p. 954. ISBN 978-0-387-31278-1.
- Liu, J.; Liu, C.; He, W. (2013), "Fluorophores and Their Applications as Molecular Probes in Living Cells", Curr. Org. Chem., 17 (6): 564–579, doi:10.2174/1385272811317060003
- Juan Carlos Stockert, Alfonso Blázquez-Castro (2017). "Chapter 4 Fluorescent Labels". Fluorescence Microscopy in Life Sciences. Bentham Science Publishers. pp. 96–134. ISBN 978-1-68108-519-7. Retrieved 24 December 2017.
- Columbia Biosciences
- Taki, Masayasu (2013). "Chapter 5. Imaging and sensing of cadmium in cells". In Astrid Sigel; Helmut Sigel; Roland K. O. Sigel (eds.). Cadmium: From Toxicology to Essentiality. Metal Ions in Life Sciences. 11. Springer. pp. 99–115. doi:10.1007/978-94-007-5179-8_5. PMID 23430772.