Table 1.1 Molecular Probes amine-reactive dyes.

FluorophoreCarboxylic Acid (COOH) *Succinimidyl Ester (SE, NHS ester) *Other *Abs (nm)Em (nm)Notes
MethoxycoumarinM1420MPM1410 340405
  • pH-insensitive alternative to 7-hydroxycoumarins
Dansyl D6104 (X)D21 (SC)340520 ‡
  • Environment-sensitive fluorescence
  • Large Stokes shift
Pyrene P130
P6114
P24 (SC)345378
  • Long excited-state lifetime
  • Spectral shifts due to excimer emission
Alexa Fluor 350 A10168 346442
  • Higher fluorescence output than AMCA
  • Optimally detected with DAPI optical filter sets
AMCA A6118 (X) 349448
  • Widely used blue-fluorescent labeling dye
  • Compact structure
Marina Blue dye M10165 365460
  • Strongly fluorescent at neutral pH
  • Optimally detected with DAPI optical filter sets
Dapoxyl dye D10161D10160 (SC)373551 ‡
  • Environment-sensitive fluorescence
  • Large Stokes shift
DialkylaminocoumarinD126
D1421
D374
D1412
 375 435470 § 475 **
  • Longer-wavelength alternatives to AMCA
BimaneB30250  380458
  • Blue-fluorescent dye
  • Small size
HydroxycoumarinH185
H1428
H1193 385445 ††
  • pH-sensitive fluorescence
  • Compact structure
Cascade Blue dye  C2284 (AA)400420
  • Resistant to quenching upon protein conjugation
  • Water soluble
Pacific Orange dye P30253 400551
  • 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
 402421
  • 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 402545
  • Large Stokes shift
  • High molar absorptivity
Pacific Blue dye P10163 410455
  • Recommended for 405 nm violet diode laser excitation
PyMPO S6110 415570
  • Large Stokes shift
Alexa Fluor 430 A10169 434539
  • Large Stokes shift
NBD S1167 (X)F486 (AH)465535
  • Environment-sensitive fluorescence
  • Compact structure
QSY 35 Q20133 475none
  • Nonfluorescent quencher
  • An efficient energy transfer acceptor from blue and green fluorophores
FluoresceinC1359
C1360
C1904 †
C2210
C6164
C1311 †
F6106 (X)
F2181 (X) †
F6129 (X) †
F6130 (EX)
C20050 (PA)
D16 (DTA)
F143 (ITC)
F1906 (ITC)
F1907 (ITC)
494518
  • 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)
495519
  • 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 488O6146O6147
O6149
O6080 (ITC) †496524
  • Photostable fluorescein substitute
  • pH-insensitive fluorescence at pH >6
BODIPY 493/503 D2191 500506
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
  • Higher 488 nm absorptivity than the BODIPY FL fluorophore
Rhodamine Green dye R6107 †
R6113 (X) †
 502527
  • Photostable fluorescein substitute
  • pH-insensitive fluorescence
BODIPY FLD2183 ‡
D3834 (C5)
D2184
D6140 (SSE)
D6102 (X)
D6184 (C5)
B10006 (STP)505513
  • BODIPY substitute for fluorescein
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
2',7'-Dichloro-
fluorescein
C368 †  510532
  • pH-insensitive fluorescence at pH >6
Oregon Green 514O6138O6139 511530
  • Exceptionally photostable
  • pH-insensitive fluorescence at pH >6
Alexa Fluor 514 A30002 † 518540
  • 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 522550
  • Succinimidyl ester derivative (6-JOE, SE; C6171MP) is widely used for oligonucleotide labeling
Eosin  E18 (ITC)524544
  • Useful for DAB photoconversion
  • Phosphorescent
Rhodamine 6G C6127
C6128
C6157 †
 525555
  • Excited by the 514 nm spectral line of the argon-ion laser
  • Spectra intermediate between those of fluorescein and tetramethylrhodamine
BODIPY R6G D6180 528550
  • BODIPY substitute with spectra similar to rhodamine 6G
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
Alexa Fluor 532 A20001
A20101MP
 531554
  • 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 534554
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
BODIPY TMR D6117 (X) 542574
  • BODIPY substitute for tetramethylrhodamine
  • pH-insensitive fluorescence
  • Narrow emission spectral bandwidth
Alexa Fluor 555 A20009
A20109
A37564
A37571
 555565
  • 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) †
555580
  • pH-insensitive fluorescence
  • Good photostability
  • Prone to aggregation
Alexa Fluor 546 A20002 †
A20102 †
 556573
  • 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 558569
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
QSY 7 Q10193 560none
  • Nonfluorescent quencher
  • Broad visible-wavelength absorption
  • Efficient energy transfer acceptor from green and orange fluorophores
QSY 9 Q20131 562none
  • 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 565571
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
Lissamine rhodamine B  L20 (SC) †
L1908 (SC) †
570590
  • Optimal for 568 nm excitation
  • Photostable
Rhodamine Red dye R6160 (X) † 570590
  • 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 576590
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
Alexa Fluor 568 A20003 †
A20103 †
 578603
  • 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-rhodamineC6124
C6156 
C6125
C6126
C1309 †
X491 (ITC) †580605
  • Succinimidyl ester derivative (6-ROX, SE; C6126) widely used for oligonucleotide labeling
BODIPY 581/591 D2228 584592
  • pH-insensitive fluorescence
  • Narrow spectral bandwidth
BODIPY TR D6116 (X) 589617
  • BODIPY substitute for the Texas Red fluorophore
  • pH-insensitive fluorescence
Alexa Fluor 594 A20004 †
A20104 †
A37565 †
A37572 †
 590617
  • 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) †
595615
  • 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
NaphthofluoresceinC652 †C653 † 605675
  • Very long-wavelength excitation and emission
  • pH-sensitive fluorescence
Alexa Fluor 610 A30050 612628
  • 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) 625640
  • pH-insensitive fluorescence
  • Ideal for excitation by the 633 nm spectral line of the He-Ne laser
Malachite green  M689 (ITC)630none
  • Nonfluorescent photosensitizer
Alexa Fluor 633 A20005 †
A20105 †
 632647
  • Far-red fluorescence
  • Good spectral separation from green fluorophores
  • pH-insensitive fluorescence between pH 4 and 10
Alexa Fluor 635   633647
  • Far-red fluorescence
  • Good spectral separation from green fluorophores
  • pH-insensitive fluorescence between pH 4 and 10
BODIPY 650/665 D10001 (X) 646660
  • pH-insensitive fluorescence
  • Longest-wavelength BODIPY dye currently available
Alexa Fluor 647 A20006
A20106
A37566
A37573
 650668
  • 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 661none
  • Nonfluorescent quencher
  • Long-wavelength absorption
  • An efficient energy transfer acceptor from red and near-infrared fluorophores
Alexa Fluor 660 A20007
A20107
 663690
  • 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
 679702
  • 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
 702723
  • 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
 749775
  • 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
 782805
  • 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.