Molecular Probes amine-reactive dyes—Table 1.1

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Fluorophore Selection Guides

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.

Molecular Probes Amine-Reactive Dyes—Table 1.1

Learn more in The Molecular Probes® Handbook

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Table 1.1 Molecular Probes amine-reactive dyes.