Table 1.1 Molecular Probes amine-reactive dyes.

Fluorophore Carboxylic Acid (COOH) * Succinimidyl Ester (SE, NHS ester) * Other * Abs (nm) Em (nm) Notes
Methoxycoumarin M1420MP M1410   340 405
  • pH-insensitive alternative to 7-hydroxycoumarins
Dansyl   D6104 (X) D21 (SC) 340 520 ‡
  • Environment-sensitive fluorescence
  • Large Stokes shift
Pyrene   P130
P6114
P24 (SC) 345 378
  • Long excited-state lifetime
  • Spectral shifts due to excimer emission
Alexa Fluor 350   A10168   346 442
  • Higher fluorescence output than AMCA
  • Optimally detected with DAPI optical filter sets
AMCA   A6118 (X)   349 448
  • Widely used blue-fluorescent labeling dye
  • Compact structure
Marina Blue dye   M10165   365 460
  • Strongly fluorescent at neutral pH
  • Optimally detected with DAPI optical filter sets
Dapoxyl dye   D10161 D10160 (SC) 373 551 ‡
  • Environment-sensitive fluorescence
  • Large Stokes shift
Dialkylaminocoumarin D126
D1421
D374
D1412
  375 435 470 § 475 **
  • Longer-wavelength alternatives to AMCA
Bimane B30250     380 458
  • Blue-fluorescent dye
  • Small size
Hydroxycoumarin H185
H1428
H1193   385 445 ††
  • pH-sensitive fluorescence
  • Compact structure
Cascade Blue dye     C2284 (AA) 400 420
  • Resistant to quenching upon protein conjugation
  • Water soluble
Pacific Orange dye   P30253   400 551
  • Excited with the 405 nm violet diode laser
  • Compatible with the Pacific Blue dye for two-color analysis using the violet diode laser
Alexa Fluor 405   A30000
A30100
  402 421
  • Cascade Blue derivative containing a spacer between the fluorophore and the reactive SE
  • Near-perfect match to the 405 nm violet diode laser
Cascade Yellow dye   C10164   402 545
  • Large Stokes shift
  • High molar absorptivity
Pacific Blue dye   P10163   410 455
  • Recommended for 405 nm violet diode laser excitation
PyMPO   S6110   415 570
  • Large Stokes shift
Alexa Fluor 430   A10169   434 539
  • Large Stokes shift
NBD   S1167 (X) F486 (AH) 465 535
  • Environment-sensitive fluorescence
  • Compact structure
QSY 35   Q20133   475 none
  • Nonfluorescent quencher
  • An efficient energy transfer acceptor from blue and green fluorophores
Fluorescein C1359
C1360
C1904 †
C2210
C6164
C1311 †
F6106 (X)
F2181 (X) †
F6129 (X) †
F6130 (EX)
C20050 (PA)
D16 (DTA)
F143 (ITC)
F1906 (ITC)
F1907 (ITC)
494 518
  • Most widely used green-fluorescent labeling dye
  • Absorption overlaps the 488 nm spectral line of the argon-ion laser
  • Prone to photobleaching
  • pH-sensitive fluorescence between pH 5–8
  • Fluorescein-5-EX succinimidyl ester (F6130) is the preferred reactive fluorescein for protein conjugation
Alexa Fluor 488   A20000 †
A20100 †
A30052 (SDP)
A30005 (TFP)
A37563 (TFP)
A37570 (TFP)
495 519
  • Bright and photostable fluorescein substitute
  • Fluorescence output unmatched by any other spectrally similar dye
  • pH-insensitive fluorescence between pH 4 and 10
  • Ideal for excitation by the 488 nm spectral line of the argon-ion laser
  • As compared with the SE, the TFP ester is less susceptible to spontaneous hydrolysis during conjugation reactions
Oregon Green 488 O6146 O6147
O6149
O6080 (ITC) † 496 524
  • Photostable fluorescein substitute
  • pH-insensitive fluorescence at pH >6
BODIPY 493/503   D2191   500 506
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
  • Higher 488 nm absorptivity than the BODIPY FL fluorophore
Rhodamine Green dye   R6107 †
R6113 (X) †
  502 527
  • Photostable fluorescein substitute
  • pH-insensitive fluorescence
BODIPY FL D2183 ‡
D3834 (C5)
D2184
D6140 (SSE)
D6102 (X)
D6184 (C5)
B10006 (STP) 505 513
  • BODIPY substitute for fluorescein
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
2',7'-Dichloro-
fluorescein
C368 †     510 532
  • pH-insensitive fluorescence at pH >6
Oregon Green 514 O6138 O6139   511 530
  • Exceptionally photostable
  • pH-insensitive fluorescence at pH >6
Alexa Fluor 514   A30002 †   518 540
  • Designed to be optically resolved from the Alexa Fluor 488 dye using spectral imaging instruments with linear-unmixing software
  • Optimal dye for the 514 nm spectral line of the argon-ion laser
4',5'-Dichloro-
2',7'-dimethoxy-
fluorescein (JOE)
  C6171MP   522 550
  • Succinimidyl ester derivative (6-JOE, SE; C6171MP) is widely used for oligonucleotide labeling
Eosin     E18 (ITC) 524 544
  • Useful for DAB photoconversion
  • Phosphorescent
Rhodamine 6G   C6127
C6128
C6157 †
  525 555
  • Excited by the 514 nm spectral line of the argon-ion laser
  • Spectra intermediate between those of fluorescein and tetramethylrhodamine
BODIPY R6G   D6180   528 550
  • BODIPY substitute with spectra similar to rhodamine 6G
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
Alexa Fluor 532   A20001
A20101MP
  531 554
  • Bright and photostable dye with spectra intermediate between those of fluorescein and tetramethylrhodamine
  • Fluorescence output unmatched by any other spectrally similar dye
  • pH-insensitive fluorescence between pH 4 and 10
  • Ideal for excitation by the 532 nm frequency-doubled principal line output of the Nd:YAG laser
BODIPY 530/550   D2187   534 554
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
BODIPY TMR   D6117 (X)   542 574
  • BODIPY substitute for tetramethylrhodamine
  • pH-insensitive fluorescence
  • Narrow emission spectral bandwidth
Alexa Fluor 555   A20009
A20109
A37564
A37571
  555 565
  • Red-orange fluorescence
  • Bright and photostable tetramethylrhodamine or Cy3 substitute
  • Spectrally similar to Cy3
Tetramethyl-
rhodamine (TMR)
C6121
C6122
C300 †
C2211
C6123
C1171 †
T6105 (X) †
T1480 (ITC)
T1481 (ITC)
T490 (ITC) †
555 580
  • pH-insensitive fluorescence
  • Good photostability
  • Prone to aggregation
Alexa Fluor 546   A20002 †
A20102 †
  556 573
  • Bright and photostable tetramethylrhodamine or Cy3 substitute
  • Fluorescence output unmatched by any other spectrally similar dye
  • pH-insensitive fluorescence between pH 4 and 10
  • Less prone to aggregation than tetramethylrhodamine
BODIPY 558/568   D2219   558 569
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
QSY 7   Q10193   560 none
  • Nonfluorescent quencher
  • Broad visible-wavelength absorption
  • Efficient energy transfer acceptor from green and orange fluorophores
QSY 9   Q20131   562 none
  • Nonfluorescent quencher
  • Spectrally similar to QSY 7, but with enhanced water solubility
  • Efficient energy-transfer acceptor from green and orange fluorophores
BODIPY 564/570   D2222   565 571
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
Lissamine rhodamine B     L20 (SC) †
L1908 (SC) †
570 590
  • Optimal for 568 nm excitation
  • Photostable
Rhodamine Red dye   R6160 (X) †   570 590
  • Conjugates are generally more fluorescent than those of Lissamine rhodamine B sulfonyl chloride, and the succinimidyl ester is more stable in H2O
BODIPY 576/589   D2225   576 590
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
Alexa Fluor 568   A20003 †
A20103 †
  578 603
  • Bright and photostable Lissamine rhodamine B substitute
  • Fluorescence output unmatched by any other spectrally similar dye
  • pH-insensitive fluorescence between pH 4 and 10
X-rhodamine C6124
C6156 
C6125
C6126
C1309 †
X491 (ITC) † 580 605
  • Succinimidyl ester derivative (6-ROX, SE; C6126) widely used for oligonucleotide labeling
BODIPY 581/591   D2228   584 592
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
BODIPY TR   D6116 (X)   589 617
  • BODIPY substitute for the Texas Red fluorophore
  • pH-insensitive fluorescence
Alexa Fluor 594   A20004 †
A20104 †
A37565 †
A37572 †
  590 617
  • Bright and photostable Texas Red dye substitute
  • Fluorescence output unmatched by any other spectrally similar dye
  • pH-insensitive fluorescence between pH 4 and 10
  • Ideal for excitation by the 594 nm spectral line of the He-Ne laser
Texas Red dye   T6134 (X) †
T20175 (X)
T353 (SC) †
T1905 (SC) †
595 615
  • Good spectral separation from green fluorophores
  • Texas Red-X succinimidyl ester typically yields higher fluorescence per attached dye than Texas Red sulfonyl chloride and is more stable in H2O
Naphthofluorescein C652 † C653 †   605 675
  • Very long-wavelength excitation and emission
  • pH-sensitive fluorescence
Alexa Fluor 610   A30050   612 628
  • Bright and photostable Texas Red dye substitute
  • Fluorescence output unmatched by any other spectrally similar dye
  • pH-insensitive fluorescence between pH 4 and 10
  • Easily differentiated from green fluorophores
  • Still visible by eye, unlike longer-wavelength fluorophores
BODIPY 630/650   D10000 (X)   625 640
  • pH-insensitive fluorescence
  • Ideal for excitation by the 633 nm spectral line of the He-Ne laser
Malachite green     M689 (ITC) 630 none
  • Nonfluorescent photosensitizer
Alexa Fluor 633   A20005 †
A20105 †
  632 647
  • Far-red fluorescence
  • Good spectral separation from green fluorophores
  • pH-insensitive fluorescence between pH 4 and 10
Alexa Fluor 635       633 647
  • Far-red fluorescence
  • Good spectral separation from green fluorophores
  • pH-insensitive fluorescence between pH 4 and 10
BODIPY 650/665   D10001 (X)   646 660
  • pH-insensitive fluorescence
  • Longest-wavelength BODIPY dye currently available
Alexa Fluor 647   A20006
A20106
A37566
A37573
  650 668
  • Far-red fluorescence
  • Produces conjugates that are brighter than those of the Cy5 dye
  • pH-insensitive fluorescence between pH 4 and 10
QSY 21   Q20132   661 none
  • Nonfluorescent quencher
  • Long-wavelength absorption
  • An efficient energy transfer acceptor from red and near-infrared fluorophores
Alexa Fluor 660   A20007
A20107
  663 690
  • Far-red fluorescence
  • Good spectral separation from green and red-orange fluorophores
  • pH-insensitive fluorescence between pH 4 and 10
Alexa Fluor 680   A20008
A20108
A37567
A37574
  679 702
  • Far-red fluorescence
  • Good separation from red fluorophores—useful for three- and four-color applications
  • pH-insensitive fluorescence between pH 4 and 10
Alexa Fluor 700   A20010
A20110
  702 723
  • Far-red fluorescence
  • Good separation from red fluorophores—useful for three- and four-color applications
  • pH-insensitive fluorescence between pH 4 and 10
Alexa Fluor 750   A20011
A20111
A37568
A37575
  749 775
  • Far-red fluorescence
  • Good separation from red fluorophores—useful for three- and four-color applications
  • pH-insensitive fluorescence between pH 4 and 10
  • Spectrally similar to the Cy7 dye
Alexa Fluor 790   A30051
A37569
  782 805
  • Spectrally similar to indocyanine green (ICG) dye
The absorption (Abs) and fluorescence emission (Em) maxima listed in this table are for the goat anti–mouse IgG antibody or dextran conjugates in aqueous buffer. Our online Fluorescence SpectraViewer (www.invitrogen.com/handbook/spectraviewer) provides an interactive utility for plotting and comparing fluorescence excitation and emission spectra for over 250 fluorophores (Using the Fluorescence SpectraViewer—Note 23.1). * COOH = carboxylic acid; SE = NHS ester = succinimidyl ester; (AA) = acetyl azide; (AH) = aryl halide; (C5) = pentanoic acid; (DTA) = dichlorotriazine; (EX) = seven-atom spacer that is more hydrophilic than X; (ITC) = isothiocyanate; (PA) = photoactivatable; (SC) = sulfonyl chloride; (SDP) = sulfodichlorophenol ester; (SSE) = sulfosuccinimidyl ester; (STP) = 4-sulfotetrafluorophenyl ester; (TFP) = tetrafluorophenyl ester; (X) = an aminohexanoyl spacer between the dye and SE. † Mixed isomers. ‡ Emission spectra of dansyl and Dapoxyl conjugates may vary considerably depending on the dye attachment site and the degree of labeling. § Spectral maxima for D374. ** Spectral maxima for D1412. †† Spectral maxima for H1193.
For Research Use Only. Not for use in diagnostic procedures.