# Fluorophore
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> Markdown URL: https://mediated.wiki/source/Fluorophore.md
> Source: https://en.wikipedia.org/wiki/Fluorophore
> Source revision: 1352401146
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{{Short description|Agents that emit light after excitation by light}}
{{for|uses and theory of fluorescence|Fluorescence in the life sciences}}
{{Cleanup list|date=February 2016}}
[[File:FISH 13 21.jpg|thumb|A fluorophore-labeled [human cell](/source/human_cell)]]
A '''fluorophore''' (or '''fluorochrome''', similarly to a [chromophore](/source/chromophore)) is a [fluorescent](/source/fluorescence) [chemical compound](/source/chemical_compound) that can re-emit light upon light excitation. Fluorophores typically contain several combined [aromatic](/source/aromaticity) groups, or planar or cyclic molecules with several [π bonds](/source/pi_bond).[{{cite book|author=Juan Carlos Stockert, Alfonso Blázquez-Castro|chapter=Chapter 3 Dyes and Fluorochromes|pages=61–95|title=Fluorescence Microscopy in Life Sciences|chapter-url=https://ebooks.benthamscience.com/book/9781681085180/|access-date=24 December 2017|year=2017|publisher=Bentham Science Publishers|isbn=978-1-68108-519-7}}]
Fluorophores are sometimes used alone, as a [tracer](/source/dye_tracing) in fluids, as a [dye](/source/dye) for [staining](/source/staining) of certain structures, as a substrate of [enzyme](/source/enzyme)s, 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](/source/covalent_bond) to [macromolecule](/source/macromolecule)s, serving as a markers (or dyes, or tags, or reporters) for affine or bioactive reagents ([antibodies](/source/antibodies), peptides, nucleic acids). Fluorophores are notably used to stain tissues, cells, or materials in a variety of analytical methods, such as [fluorescent imaging](/source/Fluorescence_microscope) and [spectroscopy](/source/fluorescence_spectroscopy).
[Fluorescein](/source/Fluorescein), via its [amine](/source/amine)-reactive [isothiocyanate](/source/isothiocyanate) derivative [fluorescein isothiocyanate](/source/fluorescein_isothiocyanate) (FITC), has been one of the most popular fluorophores. From antibody labeling, the applications have spread to nucleic acids thanks to [carboxyfluorescein](/source/carboxyfluorescein). Other historically common fluorophores are derivatives of [rhodamine](/source/rhodamine) (TRITC), [coumarin](/source/coumarin), and [cyanine](/source/cyanine).[{{cite book |author=Rietdorf J |title=Microscopic Techniques | series = Advances in Biochemical Engineering / Biotechnology |publisher=Springer |location=Berlin |date=2005 |pages= 246–9 |isbn=3-540-23698-8 |url=https://books.google.com/books?id=h9F_RGrIoicC&pg=PA247 |access-date=2008-12-13}}] Newer generations of fluorophores, many of which are proprietary, often perform better, being more photostable, brighter, or less [pH](/source/pH)-sensitive than traditional dyes with comparable excitation and emission.[{{cite book |author=Lakowicz, JR |title=Principles of fluorescence spectroscopy |edition=3rd |publisher=Springer |date=2006 |page= 954 |isbn=978-0-387-31278-1}}]
== Fluorescence ==
The fluorophore absorbs light energy of a specific wavelength and re-emits light at a longer wavelength. The absorbed [wavelength](/source/wavelength)s, [energy transfer efficiency](/source/Quantum_efficiency), and time before emission depend on both the fluorophore structure and its chemical environment, since 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 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](/source/ultraviolet) through the [visible spectrum](/source/visible_spectrum), and emission energies may continue from [visible light](/source/light) into the [near infrared](/source/near_infrared) region.
The main characteristics of fluorophores are:
* '''Maximum excitation and emission wavelength''' (expressed in [nanometer](/source/nanometer)s (nm)): corresponds to the peak in the excitation and emission spectra (usually one peak each).
* '''Molar absorption coefficient''' (in mol−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 (the 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](/source/E_(mathematical_constant)) (≈0.368) of the original amount.
* '''Stokes shift''': the difference between the maximum excitation and maximum emission wavelengths.
* '''Dark fraction''': the proportion of the molecules not active in fluorescence emission. For [quantum dots](/source/quantum_dots), prolonged single-molecule microscopy showed that 20-90% of all particles never emit fluorescence.[{{cite journal |vauthors=Pons T, Medintz IL, Farrell D, Wang X, Grimes AF, English DS, Berti L, Mattoussi H |year=2011|title= Single-molecule colocalization studies shed light on the idea of fully emitting versus dark single quantum dots |journal=Small |pmid=21710484 |doi=10.1002/smll.201100802 |volume=7 |pages=2101–2108 |issue=14 |bibcode=2011Small...7.2101P }}] On the other hand, conjugated polymer nanoparticles (Pdots) show almost no dark fraction in their fluorescence.[{{cite journal |vauthors=Koner AL, Krndija D, Hou Q, Sherratt DJ, Howarth M |year=2013|title= Hydroxy-terminated conjugated polymer nanoparticles have near-unity bright fraction and reveal cholesterol-dependence of IGF1R nanodomains |journal=ACS Nano |pmid=23330847 |doi=10.1021/nn3042122 |volume=7 |pages=1137–1144 |issue=2 |pmc=3584654|doi-access=free |bibcode=2013ACSNa...7.1137K }}] [Fluorescent protein](/source/Fluorescent_protein)s can have a dark fraction from protein misfolding or defective chromophore formation.[{{cite journal |vauthors=Garcia-Parajo MF, Segers-Nolten GM, Veerman JA, Greve J, van Hulst NF |year=2000|title= Real-time light-driven dynamics of the fluorescence emission in single green fluorescent protein molecules |journal=PNAS |pmid=10860989 |doi=10.1073/pnas.97.13.7237 |volume=97 |pages=7237–7242 |issue=13 |pmc=16529|bibcode=2000PNAS...97.7237G|doi-access=free }}]
These characteristics drive other properties, including [photobleaching](/source/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](/source/Fluorescence_anisotropy) pattern), and other factors can change the behavior of fluorophores.
Fluorophores can also be used to [quench the fluorescence](/source/Quenching_(fluorescence)) of other fluorescent dyes or to [relay their fluorescence at even longer wavelengths](/source/F%C3%B6rster_resonance_energy_transfer).
== Size (molecular weight) ==
Most fluorophores are organic [small molecule](/source/small_molecule)s of 20–100 atoms (200–1000 [Dalton](/source/Dalton_(unit)); the [molecular weight](/source/molecular_weight) may be higher depending on grafted modifications and conjugated molecules), but there are also much larger natural fluorophores that are [protein](/source/protein)s: [green fluorescent protein](/source/green_fluorescent_protein) (GFP) is 27 k[Da](/source/Dalton_(unit)), and several [phycobiliprotein](/source/phycobiliprotein)s (PE, APC...) are ≈240kDa. As of 2020, the smallest known fluorophore was claimed to be [3-hydroxyisonicotinaldehyde](/source/3-Hydroxyisonicotinaldehyde), a compound of 14 atoms and only 123 Da.[{{cite web |url=https://www.chemistryworld.com/news/fluorescent-molecule-breaks-size-record-for-green-emitting-dyes/4012911.article |title=Fluorescent molecule breaks size record for green-emitting dyes |last=Cozens |first=Tom |website=chemistryworld.com |date=2020-12-16 |access-date=2021-12-03 }}]
Fluorescence particles like [quantum dots](/source/quantum_dots) (2–10 nm diameter, 100–100,000 atoms) are also considered fluorophores.[{{cite journal|vauthors = Li Z, Zhao X, Huang C, Gong X|year = 2019|title= Recent advances in green fabrication of luminescent solar concentrators using nontoxic quantum dots as fluorophores |journal = J. Mater. Chem. C|doi=10.1039/C9TC03520F|volume=7|pages=12373–12387|issue=40| s2cid=203003761 }}]
The size of the fluorophore might [steric](/source/steric_effects)ally hinder the tagged molecule and affect the fluorescence polarity.
== Families ==
[[File:Fluorescence rainbow.JPG|thumb|Fluorescence of different substances under UV light. Green is a [fluorescein](/source/fluorescein), red is [Rhodamine B](/source/Rhodamine_B), yellow is [Rhodamine 6G](/source/Rhodamine_6G), blue is [quinine](/source/quinine), purple is a mixture of quinine and rhodamine 6g. Solutions are about 0.001% concentration in water.]]
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.[{{citation|title=Fluorophores and Their Applications as Molecular Probes in Living Cells|author=Liu, J.|author2=Liu, C.|author3=He, W.|journal=[Curr. Org. Chem.](/source/Curr._Org._Chem.)|date=2013|volume=17|issue=6|pages=564–579|doi=10.2174/1385272811317060003}}][{{cite book|author=Juan Carlos Stockert, Alfonso Blázquez-Castro|chapter=Chapter 4 Fluorescent Labels|pages=96–134|title=Fluorescence Microscopy in Life Sciences|chapter-url=https://ebooks.benthamscience.com/book/9781681085180/|access-date=24 December 2017|year=2017|publisher=Bentham Science Publishers|isbn=978-1-68108-519-7}}]
[Fluorescent protein](/source/Fluorescent_protein)s GFP, YFP, and RFP (green, yellow, and red, respectively) can be attached to other specific proteins to form a [fusion protein](/source/fusion_protein), synthesized in cells after [transfection](/source/transfection) of a suitable [plasmid](/source/plasmid) carrier.
'''Non-protein''' organic fluorophores belong to following major chemical families:
* '''[Xanthene](/source/Xanthene) derivatives:''' [fluorescein](/source/fluorescein), [rhodamine](/source/rhodamine), [Oregon green](/source/Oregon_green), [eosin](/source/eosin), and [Texas red](/source/Texas_red)
* '''[Cyanine](/source/Cyanine) derivatives:''' cyanine, [indocarbocyanine](/source/Indocyanine_green), [oxacarbocyanine](/source/oxacarbocyanine), [thiacarbocyanine](/source/thiacarbocyanine), and [merocyanine](/source/merocyanine)
* '''[Squaraine](/source/Squaraine) derivatives and ring-substituted squaraines''', including Seta and Square dyes
* '''[Squaraine rotaxane](/source/Squaraine_Rotaxane) derivatives:''' See Tau dyes
* '''[Naphthalene](/source/Naphthalene) derivatives''' ([dansyl](/source/Dansyl_chloride) and [prodan](/source/6-Propionyl-2-Dimethylaminonaphthalene) derivatives)
* '''[Coumarin](/source/Coumarin) derivatives'''
* '''[Oxadiazole](/source/Furazan) derivatives:''' [pyridyloxazole](/source/pyridyloxazole), [nitrobenzoxadiazole](/source/NBD-TMA), and [benzoxadiazole](/source/benzoxadiazole)
* '''[Anthracene](/source/Anthracene) derivatives:''' [anthraquinone](/source/anthraquinone)s, including DRAQ5, DRAQ7, and CyTRAK Orange
* '''[Pyrene](/source/Pyrene) derivatives:''' [cascade blue](/source/cascade_blue), etc.
* '''[Oxazine](/source/Oxazine) derivatives:''' [Nile red](/source/Nile_red), [Nile blue](/source/Nile_blue), [cresyl violet](/source/cresyl_violet), [oxazine 170](/source/oxazine_170), etc.
* '''[Acridine](/source/Acridine) derivatives:''' [proflavin](/source/proflavin), [acridine orange](/source/acridine_orange), [acridine yellow](/source/acridine_yellow), etc.
* '''[Arylmethine](/source/Arylmethine) derivatives:''' [auramine](/source/auramine), [crystal violet](/source/crystal_violet), [malachite green](/source/malachite_green)
* '''[Tetrapyrrole](/source/Tetrapyrrole) derivatives:''' [porphin](/source/porphin), [phthalocyanine](/source/phthalocyanine), [bilirubin](/source/bilirubin)
* '''Dipyrromethene derivatives:''' [BODIPY](/source/BODIPY), [aza-BODIPY](/source/Azadipyrromethene)
These fluorophores fluoresce due to [delocalized electron](/source/delocalized_electron)s which can jump a [band](/source/Electronic_band_structure) and stabilize the energy absorbed. For example, [benzene](/source/benzene), one of the simplest aromatic hydrocarbons, is excited at 254 nm and emits at 300 nm.[[http://omlc.ogi.edu/spectra/PhotochemCAD/html/benzene.html Omlc.ogi.edu]] This discriminates fluorophores from quantum dots, which are fluorescent semiconductor [nanoparticle](/source/nanoparticle)s.
They can be attached to proteins to specific functional groups, such as [amino](/source/amino) groups ([active ester](/source/active_ester), [carboxylate](/source/carboxylate), [isothiocyanate](/source/isothiocyanate), [hydrazine](/source/hydrazine)), [carboxyl](/source/carboxyl) groups ([carbodiimide](/source/carbodiimide)), [thiol](/source/thiol) ([maleimide](/source/maleimide), [acetyl bromide](/source/acetyl_bromide)), and [organic azide](/source/organic_azide) (via [click chemistry](/source/click_chemistry) or non-specifically ([glutaraldehyde](/source/glutaraldehyde))).
Additionally, various functional groups can be present to alter their properties, such as solubility, or confer special properties, such as [boronic acid](/source/boronic_acid) which binds to sugars or multiple [carboxyl group](/source/carboxyl_group)s 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](/source/Solvatochromism)), 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](/source/fura-2AM) and [fluorescein-diacetate](/source/fluorescein-diacetate).
The following dye families are '''trademark groups''', and do not necessarily share structural similarities.
[[File:DAPIMitoTrackerRedAlexaFluor488BPAE.jpg|thumb|Bovine Pulmonary Artery Endothelial cell nuclei stained blue with [DAPI](/source/DAPI), [mitochondria](/source/mitochondria) stained red with MitoTracker Red CMXRos, and [F-actin](/source/F-actin) stained green with Alexa Fluor 488 [phalloidin](/source/phalloidin) and imaged on a fluorescent microscope.]]
* [CF dye](/source/CF_dye) (Biotium)
* DRAQ and CyTRAK probes (BioStatus)
* [BODIPY](/source/BODIPY) ([Invitrogen](/source/Invitrogen))
* [EverFluor](/source/EverFluor) (Setareh Biotech)
* [Alexa Fluor](/source/Alexa_Fluor) (Invitrogen)
* [Bella Fluor](/source/Bella_Fluor) (Setareh Biotech)
* [DyLight Fluor](/source/DyLight_Fluor) (Thermo Scientific, Pierce)
* [Atto](/source/ATTO_dyes) (ATTO-TEC GmbH)
* Tracy ([Sigma Aldrich](/source/Sigma_Aldrich))
* [FluoProbes](/source/Fluoprobes) ([Interchim](/source/Interchim))
* [Abberior Dyes](/source/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](/source/Biosearch_Technologies))
* SureLight Dyes ([APC](/source/Allophycocyanin), RPE[PerCP](/source/Peridinin), [Phycobilisomes](/source/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===
{| class="wikitable sortable"
|-
! Dye
! Ex (nm)
! Em (nm)
! MW
! Notes
|-
| [Hydroxycoumarin](/source/Hydroxycoumarin)
| 325
| 386
| 331
| Succinimidyl ester
|-
| [Aminocoumarin](/source/Aminocoumarin)
| 350
| 445
| 330
| Succinimidyl ester
|-
| [Methoxycoumarin](/source/Methoxycoumarin)
| 360
| 410
| 317
| Succinimidyl ester
|-
| [Cascade Blue](/source/Cascade_Blue)
| (375);401
| 423
| 596
| Hydrazide
|-
| [Pacific Blue](/source/Pacific_Blue_(dye))
| 403
| 455
| 406
| Maleimide
|-
| [Pacific Orange](/source/Pacific_Orange)
| 403
| 551
|
|
|-
| [3-Hydroxyisonicotinaldehyde](/source/3-Hydroxyisonicotinaldehyde)
| 385
| 525
| 123
| QY 0.15; pH sensitive
|-
| [Lucifer yellow](/source/Lucifer_yellow)
| 425
| 528
|
|
|-
| NBD
| 466
| 539
| 294
| NBD-X
|-
| [R-Phycoerythrin](/source/R-Phycoerythrin) (PE)
| 480;565
| 578
| 240 k
|
|-
| PE-Cy5 conjugates
| 480;565;650
| 670
|
| aka Cychrome, R670, Tri-Color, Quantum Red
|-
| PE-Cy7 conjugates
| 480;565;743
| 767
|
|
|-
| [Red 613](/source/Red_613)
| 480;565
| 613
|
| PE-Texas Red
|-
| PerCP
| 490
| 675
| 35kDa
| Peridinin chlorophyll protein
|-
| [TruRed](/source/TruRed)
| 490,675
| 695
|
| PerCP-Cy5.5 conjugate
|-
| FluorX
| 494
| 520
| 587
| (GE Healthcare)
|-
| [Fluorescein](/source/Fluorescein)
| 495
| 519
| 389
| FITC; pH sensitive
|-
| BODIPY-FL
| 503
| 512
|
|
|-
|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
|-
| Cy2
| 489
| 506
| 714
| QY 0.12
|-
| Cy3
| (512);550
| 570;(615)
| 767
| QY 0.15
|-
| Cy3B
| 558
| 572;(620)
| 658
| QY 0.67
|-
| Cy3.5
| 581
| 594;(640)
| 1102
| QY 0.15
|-
| Cy5
| (625);650
| 670
| 792
| QY 0.28
|-
| Cy5.5
| 675
| 694
| 1272
| QY 0.23
|-
| Cy7
| 743
| 767
| 818
| QY 0.28
|-
| TRITC
| 547
| 572
| 444
| TRITC
|-
| [X-Rhodamine](/source/X-Rhodamine)
| 570
| 576
| 548
| XRITC
|-
| [Lissamine Rhodamine B](/source/Lissamine_Rhodamine_B)
| 570
| 590
|
|
|-
| [Texas Red](/source/Texas_Red)
| 589
| 615
| 625
| Sulfonyl chloride
|-
| Allophycocyanin (APC)
| 650
| 660
| 104 k
|
|-
| APC-Cy7 conjugates
| 650;755
| 767
|
| Far Red
|}
Abbreviations:
*Ex (nm): Excitation wavelength in [nanometers](/source/nanometers)
*Em (nm): Emission wavelength in nanometers
*MW: [Molecular weight](/source/Molecular_weight)
*QY: [Quantum yield](/source/Quantum_yield)
===Nucleic acid dyes===
{| class="wikitable sortable"
|-
! Dye
! Ex (nm)
! Em (nm)
! MW
! Notes
|-
| [Hoechst](/source/Hoechst_stain) 33342
| 343
| 483
| 616
| AT-selective
|-
| [DAPI](/source/DAPI)
| 345
| 455
|
| AT-selective
|-
| [Hoechst](/source/Hoechst_stain) 33258
| 345
| 478
| 624
| AT-selective
|-
| [SYTOX](/source/SYTOX) Blue
| 431
| 480
| ~400
| DNA
|-
| [Chromomycin A3](/source/Chromomycin_A3)
| 445
| 575
|
| CG-selective
|-
| [Mithramycin](/source/Mithramycin)
| 445
| 575
|
|
|-
| [YOYO-1](/source/YOYO-1)
| 491
| 509
| 1271
|
|-
| [Ethidium Bromide](/source/Ethidium_Bromide)
| 210;285
| 605
| 394
| in aqueous solution
|-
|[GelRed](/source/GelRed)
|290;520
|595
|1239
|Non-toxic substitute for Ethidium Bromide
|-
| [Acridine Orange](/source/Acridine_orange)
| 503
| 530/640
|
| DNA/RNA
|-
| [SYTOX](/source/SYTOX) Green
| 504
| 523
| ~600
| DNA
|-
| TOTO-1, TO-PRO-1
| 509
| 533
|
| Vital stain, TOTO: Cyanine Dimer
|-
| TO-PRO: Cyanine Monomer
|-
| [Thiazole Orange](/source/Thiazole_Orange)
| 510
| 530
|
|
|-
| CyTRAK Orange
| 520
| 615
| -
| (Biostatus) (red excitation dark)
|-
| [Propidium Iodide](/source/Propidium_Iodide) (PI)
| 536
| 617
| 668.4
|
|-
| LDS 751
| 543;590
| 712;607
| 472
| DNA (543ex/712em), RNA (590ex/607em)
|-
| [7-AAD](/source/7-AAD)
| 546
| 647
|
| 7-aminoactinomycin D, CG-selective
|-
| [SYTOX](/source/SYTOX) Orange
| 547
| 570
| ~500
| DNA
|-
| TOTO-3, TO-PRO-3
| 642
| 661
|
|
|-
| 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===
{| class="wikitable sortable"
|-
! Dye
! Ex (nm)
! Em (nm)
! MW
! Notes
|-
|Indo-1
| 361/330
| 490/405
| 1010
| AM ester, low/high calcium (Ca2+)
|-
| [Fluo-3](/source/Fluo-3)
| 506
| 526
| 855
| AM ester. pH > 6
|-
| [Fluo-4](/source/Fluo-4)
| 491/494
| 516
| 1097
| AM ester. pH 7.2
|-
| DCFH
| 505
| 535
| 529
| [2'7'Dichorodihydrofluorescein](/source/2'7'Dichorodihydrofluorescein), oxidized form
|-
| DHR
| 505
| 534
| 346
| [Dihydrorhodamine 123](/source/Dihydrorhodamine_123), oxidized form, light catalyzes oxidation
|-
| [SNARF](/source/Seminaphtharhodafluor)
| 548/579
| 587/635
|
| pH 6/9
|}
===Fluorescent proteins===
{| class="wikitable sortable"
|-
! Dye
! Ex (nm)
! Em (nm)
! MW
! QY
! BR
! PS
! Notes
|-
| GFP (Y66H mutation)
| 360
| 442
|
|
|
|
|
|-
| GFP (Y66F mutation)
| 360
| 508
|
|
|
|
|
|-
| EBFP
| 380
| 440
|
| 0.18
| 0.27
|
| monomer
|-
| EBFP2
| 383
| 448
|
|
| 20
|
| monomer
|-
| Azurite
| 383
| 447
|
|
| 15
|
| monomer
|-
| GFPuv
| 385
| 508
|
|
|
|
|
|-
| [T-Sapphire](/source/T-Sapphire)
| 399
| 511
|
| 0.60
| 26
| 25
| weak dimer
|-
| [Cerulean](/source/Green_fluorescent_protein)
| 433
| 475
|
| 0.62
| 27
| 36
| weak dimer
|-
| mCFP
| 433
| 475
|
| 0.40
| 13
| 64
| monomer
|-
| mTurquoise2
| 434
| 474
|
| 0.93
| 28
|
| monomer
|-
| ECFP
| 434
| 477
|
| 0.15
| 3
|
|
|-
| CyPet
| 435
| 477
|
| 0.51
| 18
| 59
| weak dimer
|-
| GFP (Y66W mutation)
| 436
| 485
|
|
|
|
|
|-
| mKeima-Red
| 440
| 620
|
| 0.24
| 3
|
| monomer (MBL)
|-
| TagCFP
| 458
| 480
|
|
| 29
|
| dimer (Evrogen)
|-
| AmCyan1
| 458
| 489
|
| 0.75
| 29
|
| tetramer, (Clontech)
|-
| mTFP1
| 462
| 492
|
|
| 54
|
| dimer
|-
| GFP (S65A mutation)
| 471
| 504
|
|
|
|
|
|-
| [Midoriishi Cyan](/source/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)
|-
| TagGFP
| 482
| 505
|
|
| 34
|
| monomer (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](/source/Azami_Green)
| 492
| 505
|
| 0.74
| 41
|
| monomer (MBL)
|-
| ZsGreen1
| 493
| 505
| 105k
| 0.91
| 40
|
| tetramer, (Clontech)
|-
| TagYFP
| 508
| 524
|
|
| 47
|
| monomer (Evrogen)
|-
| EYFP
| 514
| 527
| 26k
| 0.61
| 51
| 60
| weak dimer, (Clontech)
|-
| Topaz
| 514
| 527
|
|
| 57
|
| monomer
|-
| Venus
| 515
| 528
|
| 0.57
| 53
| 15
| weak dimer
|-
| mCitrine
| 516
| 529
|
| 0.76
| 59
| 49
| monomer
|-
| YPet
| 517
| 530
|
| 0.77
| 80
| 49
| weak dimer
|-
| TurboYFP
| 525
| 538
| 26 k
| 0.53
| 55.7
|
| dimer, (Evrogen)
|-
| ZsYellow1
| 529
| 539
|
| 0.65
| 13
|
| tetramer, (Clontech)
|-
| [Kusabira Orange](/source/Kusabira_Orange)
| 548
| 559
|
| 0.60
| 31
|
| monomer (MBL)
|-
| mOrange
| 548
| 562
|
| 0.69
| 49
| 9
| monomer
|-
| [Allophycocyanin](/source/Allophycocyanin) (APC)
| 652
| 657.5
| 105 kDa
| 0.68
|
|
| heterodimer, crosslinked[{{Cite web |url=http://www.columbiabiosciences.com/technical-info/ |title=Columbia Biosciences |access-date=2014-06-07 |archive-date=2024-08-21 |archive-url=https://web.archive.org/web/20240821214555/http://www.columbiabiosciences.com/technical-info/ |url-status=dead }}]
|-
| mKO
| 548
| 559
|
| 0.60
| 31
| 122
| monomer
|-
| TurboRFP
| 553
| 574
| 26 k
| 0.67
| 62
|
| dimer, (Evrogen)
|-
| tdTomato
| 554
| 581
|
| 0.69
| 95
| 98
| tandem dimer
|-
| TagRFP
| 555
| 584
|
|
| 50
|
| monomer (Evrogen)
|-
| DsRed monomer
| 556
| 586
| ~28k
| 0.1
| 3.5
| 16
| monomer, (Clontech)
|-
| DsRed2 ("RFP")
| 563
| 582
| ~110k
| 0.55
| 24
|
| (Clontech)
|-
| mStrawberry
| 574
| 596
|
| 0.29
| 26
| 15
| monomer
|-
| TurboFP602
| 574
| 602
| 26 k
| 0.35
| 26
|
| dimer, (Evrogen)
|-
| AsRed2
| 576
| 592
| ~110k
| 0.21
| 13
|
| tetramer, (Clontech)
|-
| mRFP1
| 584
| 607
| ~30k
| 0.25
|
|
| monomer, ([Tsien lab](/source/Roger_Tsien))
|-
| J-Red
| 584
| 610
|
| 0.20
| 8.8
| 13
| dimer
|-
| [R-phycoerythrin](/source/phycoerythrin) (RPE)
| 565 >498
| 573
| 250 kDa
| 0.84
|
|
| heterotrimer[{{Cite journal|last1=Bindels|first1=Daphne S.|last2=Haarbosch|first2=Lindsay|last3=van Weeren|first3=Laura|last4=Postma|first4=Marten|last5=Wiese|first5=Katrin E.|last6=Mastop|first6=Marieke|last7=Aumonier|first7=Sylvain|last8=Gotthard|first8=Guillaume|last9=Royant|first9=Antoine|last10=Hink|first10=Mark A.|last11=Gadella|first11=Theodorus W. J.|date=January 2017|title=mScarlet: a bright monomeric red fluorescent protein for cellular imaging|url=https://www.nature.com/articles/nmeth.4074|journal=Nature Methods|language=en|volume=14|issue=1|pages=53–56|doi=10.1038/nmeth.4074|pmid=27869816|bibcode=2017NatCB..14...53B |s2cid=3539874|issn=1548-7105|url-access=subscription}}]
|}
=== Advanced fluorescent proteins ===
'''StayGold''' and '''mStayGold''' are advanced fluorescent proteins that have significantly contributed to the field of live-cell imaging. StayGold, known for its high photostability and brightness, was originally designed as a dimeric fluorescent protein, which, while effective, posed challenges related to the aggregation and labelling accuracy.[{{Cite journal |last1=Hirano |first1=Masahiko |last2=Ando |first2=Ryoko |last3=Shimozono |first3=Satoshi |last4=Sugiyama |first4=Mayu |last5=Takeda |first5=Noriyo |last6=Kurokawa |first6=Hiroshi |last7=Deguchi |first7=Ryusaku |last8=Endo |first8=Kazuki |last9=Haga |first9=Kei |last10=Takai-Todaka |first10=Reiko |last11=Inaura |first11=Shunsuke |last12=Matsumura |first12=Yuta |last13=Hama |first13=Hiroshi |last14=Okada |first14=Yasushi |last15=Fujiwara |first15=Takahiro |date=July 2022 |title=A highly photostable and bright green fluorescent protein |journal=Nature Biotechnology |language=en |volume=40 |issue=7 |pages=1132–1142 |doi=10.1038/s41587-022-01278-2 |issn=1546-1696 |pmc=9287174 |pmid=35468954}}] To address these limitations, mStayGold was engineered as a monomeric variant, enhancing its utility in precise protein labeling. mStayGold exhibits superior photostability, maintaining fluorescence under high irradiance conditions and demonstrates increased brightness compared to its former variant StayGold. Additionally, it matures faster, allowing for quicker imaging post-transfection. These advancements make mStayGold a versatile tool for a variety of applications, including single molecule tracking and high resolution imaging of dynamic cellular processes, thereby expanding the capabilities of fluorescent protein in biological research.[{{Cite journal |last1=Ando |first1=Ryoko |last2=Shimozono |first2=Satoshi |last3=Ago |first3=Hideo |last4=Takagi |first4=Masatoshi |last5=Sugiyama |first5=Mayu |last6=Kurokawa |first6=Hiroshi |last7=Hirano |first7=Masahiko |last8=Niino |first8=Yusuke |last9=Ueno |first9=Go |last10=Ishidate |first10=Fumiyoshi |last11=Fujiwara |first11=Takahiro |last12=Okada |first12=Yasushi |last13=Yamamoto |first13=Masaki |last14=Miyawaki |first14=Atsushi |date=April 2024 |title=StayGold variants for molecular fusion and membrane-targeting applications |journal=Nature Methods |language=en |volume=21 |issue=4 |pages=648–656 |doi=10.1038/s41592-023-02085-6 |issn=1548-7105 |pmc=11009113 |pmid=38036853}}]
Abbreviations:
*Ex (nm): Excitation wavelength in [nanometers](/source/nanometers)
*Em (nm): Emission wavelength in nanometers
*MW: [Molecular weight](/source/Molecular_weight)
*QY: [Quantum yield](/source/Quantum_yield)
*BR: Brightness: Molar absorption coefficient * quantum yield / 1000
*PS: [Photostability](/source/Photostability): time [sec] to reduce brightness by 50%
== Applications ==
{{further|Fluorescence in the life sciences}}
Fluorophores have particular importance in the field of [biochemistry](/source/biochemistry) and [protein](/source/protein) studies, for example, in [immunofluorescence](/source/immunofluorescence), cell analysis,[{{Cite journal|last1=Sirbu|first1=Dumitru|last2=Luli|first2=Saimir|last3=Leslie|first3=Jack|last4=Oakley|first4=Fiona|last5=Benniston|first5=Andrew C.|date=2019|title=Enhanced in vivo Optical Imaging of the Inflammatory Response to Acute Liver Injury in C57BL/6 Mice Using a Highly Bright Near-Infrared BODIPY Dye|journal=ChemMedChem|language=en|volume=14|issue=10|pages=995–999|doi=10.1002/cmdc.201900181|pmid=30920173|s2cid=85544665|issn=1860-7187}}] [immunohistochemistry](/source/immunohistochemistry),[{{cite book |author = Tsien RY|author2 = Waggoner A|editor=Pawley JB |chapter= Fluorophores for confocal microscopy | title=Handbook of biological confocal microscopy |publisher=Plenum Press |location=New York |date=1995 |pages=267–74 |isbn=0-306-44826-2 |chapter-url=https://books.google.com/books?id=16Ft5k8RC-AC&pg=PA267|access-date=2008-12-13}}][{{cite book
|last1=Taki
|first1=Masayasu
|editor=Astrid Sigel
|editor2=Helmut Sigel
|editor3=Roland K. O. Sigel
|title=Cadmium: From Toxicology to Essentiality
|series=Metal Ions in Life Sciences
|volume=11
|pages=99–115
|date=2013
|publisher=Springer
|chapter=Chapter 5. Imaging and sensing of cadmium in cells
|doi=10.1007/978-94-007-5179-8_5|pmid=23430772
|isbn=978-94-007-5178-1
}}
] and [small molecule sensors](/source/small_molecule_sensors).[{{Cite journal|last1=Sirbu|first1=Dumitru|last2=Butcher|first2=John B.|last3=Waddell|first3=Paul G.|last4=Andras|first4=Peter|last5=Benniston|first5=Andrew C.|date=2017-09-18|title=Locally Excited State-Charge Transfer State Coupled Dyes as Optically Responsive Neuron Firing Probes|journal=Chemistry - A European Journal|volume=23|issue=58|pages=14639–14649|doi=10.1002/chem.201703366|pmid=28833695|bibcode=2017ChEuJ..2314639S |issn=0947-6539|url=https://publications.aston.ac.uk/id/eprint/40362/1/Locally_Excited_State_Charge_Transfer_State.pdf}}][{{Cite journal|last1=Jiang|first1=Xiqian|last2=Wang|first2=Lingfei|last3=Carroll|first3=Shaina L.|last4=Chen|first4=Jianwei|last5=Wang|first5=Meng C.|last6=Wang|first6=Jin|date=2018-08-20|title=Challenges and Opportunities for Small-Molecule Fluorescent Probes in Redox Biology Applications|journal=Antioxidants & Redox Signaling|volume=29|issue=6|pages=518–540|doi=10.1089/ars.2017.7491|issn=1523-0864|pmc=6056262|pmid=29320869}}]
=== Fluorescent polymers ===
Fluorophores have been used with polymers in different ways and for many types of applications in different fields such as [biochemistry](/source/biochemistry), [analytical chemistry](/source/analytical_chemistry), [material science](/source/Materials_science), and [nanochemistry](/source/nanochemistry). For example, [peptide](/source/peptide)-[RAFT](/source/Reversible_addition%E2%88%92fragmentation_chain-transfer_polymerization) agents tagged with [5,6-carboxyfluorescein](/source/6-Carboxyfluorescein) have been used to synthesize [polyacrylamide](/source/polyacrylamide), [polyacrylate](/source/Acrylate_polymer) and [polystyrene](/source/polystyrene) with possible applications for analysis of cellular uptake of different sized polymers[{{Cite journal |last=Shaw |first=Paige A. |last2=Klausen |first2=Maxime |last3=Lilienkampf |first3=Annamaria |last4=Bradley |first4=Mark |date=2023-09-11 |title=Fluorophore-Tagged Poly-Lysine RAFT Agents: Controlled Synthesis of Trackable Cell-Penetrating Peptide–Polymers |url=https://doi.org/10.1021/acsmacrolett.3c00460 |journal=ACS Macro Letters |volume=12 |issue=10 |pages=1280–1285 |doi=10.1021/acsmacrolett.3c00460 |issn=2161-1653}}]. Fluorescent [polyolefins](/source/Polyolefin), such as fluorescent [polyethylene](/source/polyethylene), have been synthesized and explored as [materials](/source/Material) due to their possible applications in fluorescent probes, [LEDs](/source/Light-emitting_diode), [information storage](/source/Data_storage) and [encryption](/source/encryption) devices, cell imaging, [plastic](/source/plastic) sorting, and [quantification](/source/Quantification_(science)) of [recycled plastic](/source/Plastic_recycling)[{{Cite journal |last=Wei |first=Shuang |last2=Zhang |first2=Zongnan |last3=Xu |first3=Yanzi |last4=Dang |first4=Dongfeng |last5=Zeng |first5=Rong |date=2024-04-11 |title=Covalent Installation of Fluorophores into Polyethylene: Synthesis, Characterization, and Applications |url=https://doi.org/10.1021/acs.macromol.4c00381 |journal=Macromolecules |volume=57 |issue=8 |pages=3595–3603 |doi=10.1021/acs.macromol.4c00381 |issn=0024-9297|url-access=subscription }}].
== Uses outside the life sciences ==
thumb|right|Fluorescent sea dye
Fluorescent dyes find a wide use in industry, going under the name of "neon colors", such as:
* Multi-ton scale usages in textile dyeing and optical brighteners in [laundry detergent](/source/laundry_detergent)s
* Advanced [cosmetic](/source/cosmetics) formulations
* [Safety equipment](/source/Safety_equipment) and clothing
* [Organic light-emitting diode](/source/Organic_light-emitting_diode)s (OLEDs)
* Fine arts and design (posters and paintings)
* Synergists for insecticides and experimental drugs
* Dyes in [highlighter](/source/highlighter)s to give off a glow-like effect
* [Solar panel](/source/Solar_panel)s to collect more light / wavelengths
* Fluorescent sea dye is used to help airborne [search and rescue](/source/search_and_rescue) teams locate objects in the water
== See also ==
* [:Category:Fluorescent dyes](/source/%3ACategory%3AFluorescent_dyes)
* [Fluorescence in the life sciences](/source/Fluorescence_in_the_life_sciences)
* [Quenching of fluorescence](/source/Quenching_(fluorescence))
* [Fluorescence recovery after photobleaching](/source/Fluorescence_recovery_after_photobleaching) (FRAP) - an application for quantifying mobility of molecules in [lipid bilayer](/source/lipid_bilayer)s.
== References ==
{{Reflist|30em}}
== External links ==
* [https://archive.today/20121205013840/http://www.fluorophores.org/ The Database of fluorescent dyes]
* [https://web.archive.org/web/20141020225338/http://pingu.salk.edu/flow/fluo.html Table of fluorochromes]
* [http://www.invitrogen.com/site/us/en/home/References/Molecular-Probes-The-Handbook.html The Molecular Probes Handbook] - a comprehensive resource for fluorescence technology and its applications.
Category:Dyes
Category:Luminescence
---
Adapted from the Wikipedia article [Fluorophore](https://en.wikipedia.org/wiki/Fluorophore) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Fluorophore?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.