Invitrogen - Molecular Probes - Table 1.1 - Molecular Probes' amine-reactive dyes

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Updated: October 21, 2005

Table 1.1 — Molecular Probes' amine-reactive dyes

Fluorophore	COOH *	SE *	Other *	Abs (nm)	Em (nm)	Notes
Alexa Fluor 350		A10168		346	442	Higher fluorescence per attached dye than AMCA
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 spectral line of the blue diode laser
Alexa Fluor 430		A10169		433	539	Large Stokes shift
Alexa Fluor 488		A20000 A20100	A30005 (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
Alexa Fluor 500		A30001		503	525	Designed to be optically separated from the Alexa Fluor 514 dye using the Zeiss META system or similar spectral imaging instruments with linear-unmixing software
Alexa Fluor 514		A30002		518	540	Designed to be optically separated from the Alexa Fluor 500 or the Alexa Fluor 488 dye using the Zeiss META system or similar spectral imaging instruments with linear-unmixing software Optimal dye for the 514 nm spectral line of the argon-ion laser
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
Alexa Fluor 546		A20002 A20102		556	575	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 Ideal for excitation by the 546 nm spectral line of the mercury-arc lamp
Alexa Fluor 555		A20009 A20109		555	565	Red-orange fluorescence Bright and photostable tetramethylrhodamine or Cy3 substitute Spectrally identical to Cy3
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 Ideal for excitation by the 568 nm spectral line of the Ar–Kr mixed-gas laser
Alexa Fluor 594		A20004 A20104		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
Alexa Fluor 610		A30003 A30103		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
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 Absorption spectra does not split into two peaks upon protein conjugation Good spectral separation from green fluorophores pH-insensitive fluorescence between pH 4 and 10
Alexa Fluor 647		A20006 A20106		650	668	Far-red fluorescence Produces conjugates that are brighter than those of the Cy5 dye pH-insensitive fluorescence between pH 4 and 10
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		682	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		696	719	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		752	779	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
AMCA		A6118 (X)		349	448	Widely used blue-fluorescent labeling dye Compact structure
Bimane	B30250	B30251		380	458	Blue-fluorescent dye Small size
BODIPY 493/503		D2191		500	506	pH-insensitive fluorescence Narrow spectral bandwidth Higher 488 nm absorptivity than the BODIPY FL fluorophore
BODIPY FL	D2183 D3834 (C₅)	D2184 D6140 (SSE) D6141 (CASE) D6102 (X) D6184 (C₅)	B10006 (STP)	505	513	BODIPY substitute for fluorescein pH-insensitive fluorescence Narrow spectral bandwidth Succinimidyl ester with a cysteic acid spacer (BODIPY FL, CASE; D6141) is the preferred reactive BODIPY FL dye for protein conjugation
BODIPY R6G		D6180		528	550	BODIPY substitute with spectra similar to rhodamine 6G pH-insensitive fluorescence Narrow spectral bandwidth
BODIPY 530/550		D2187		534	554	pH-insensitive fluorescence Narrow spectral bandwidth
BODIPY TMR		D6117 (X)	B10002 (STP)	542	574	BODIPY substitute for tetramethylrhodamine pH-insensitive fluorescence Narrow spectral bandwidth
BODIPY 558/568		D2219		558	569	pH-insensitive fluorescence Narrow spectral bandwidth
BODIPY 564/570		D2222		565	571	pH-insensitive fluorescence Narrow spectral bandwidth
BODIPY 576/589		D2225		576	590	pH-insensitive fluorescence Narrow spectral bandwidth
BODIPY 581/591		D2228		584	592	pH-insensitive fluorescence Narrow spectral bandwidth
BODIPY TR		D6116 (X)	B10003 (STP)	589	617	BODIPY substitute for the Texas Red fluorophore pH-insensitive fluorescence
BODIPY 630/650		D10000 (X)		625	640	pH-insensitive fluorescence Ideal for excitation by the 633 nm spectral line of the He–Ne laser
BODIPY 650/665		D10001 (X)	B10005 (STP)	646	660	pH-insensitive fluorescence Longest-wavelength BODIPY dye currently available Ideal for excitation by the 647 nm spectral line of the krypton-ion laser
2',4,4',5',7,7'-hexachlorofluorescein (HEX)		C20091 (SE)		535	556	Succinimidyl ester derivative (6-HEX, SE; C20091) is widely used for automated DNA sequencing
Cascade Blue dye			C2284 (AA)	400	420	Resistant to quenching upon protein conjugation Water soluble
Cascade Yellow dye		C10164		402	545	Large Stokes shift High molar absorptivity
Dansyl		D6104 (X)	D21 (SC)	340	520	Environment-sensitive fluorescence Large Stokes shift
Dapoxyl dye		D10161 D10162	D10160 (SC)	373	551	Environment-sensitive fluorescence Large Stokes shift
Dialkylaminocoumarin	D126 D1421	D374 D1412		375 435	470 § 475 **	Longer-wavelength alternatives to AMCA
4',5'-Dichloro- 2',7'-dimethoxy- fluorescein (JOE)		C6171MP		522	550	Succinimidyl ester derivative (6-JOE, SE; C6171MP) is widely used for automated DNA sequencing
2',7'-Dichloro- fluorescein	C368			510	532	pH-insensitive fluorescence at pH >6
Eosin			E18 (ITC)	524	544	Useful for DAB photoconversion Phosphorescent
Erythrosin			E30150 (ITC)	530	555	Phosphorescent
Fluorescein	C1359 C1360 C1904	C2210 C6164 C1311 F6106 (X) F2181 (X) F6129 (X) F6130 (EX) C20050 (C)	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 Succinimidyl ester derivative (5-FAM, SE; C2210) is widely used for automated DNA sequencing Fluorescein-5-EX succinimidyl ester (F6130) is the preferred reactive fluorescein for protein conjugation
Hydroxycoumarin	H185 H1428	H1193		385	445	pH-sensitive fluorescence Compact structure
Lissamine rhodamine B			L20 (SC) L1908 (SC)	570	590	Optimal for 568 nm excitation Photostable
Malachite green			M689 (ITC)	630	none	Nonfluorescent photosensitizer
Marina Blue dye		M10165		365	460	Strongly fluorescent at neutral pH, unlike 7-hydroxycoumarins Optimal for 365 nm excitation of the mercury-arc lamp
Methoxycoumarin	M1420MP	M1410		340	405	pH-insensitive alternative to 7-hydroxycoumarins
Naphthofluorescein	C652	C653		605	675	Very long-wavelength excitation and emission pH-sensitive fluorescence
NBD		S1167 (X)	F486 (AH)	465	535	Environment-sensitive fluorescence Compact structure
Oregon Green 488	O6146	O6147 O6149	O6080 (ITC)	496	524	Photostable fluorescein substitute pH-insensitive fluorescence at pH >6
Oregon Green 514	O6138	O6139		511	530	Exceptionally photostable pH-insensitive fluorescence at pH >6
Pacific Blue dye		P10163		410	455	Strongly fluorescent at neutral pH, unlike 7-hydroxycoumarins
Pacific Orange dye		P30253		400	551	Excited with the violet laser Compatible with the Pacific Blue dye for two-color analysis using the violet laser
PyMPO		S6110		415	570	Large Stokes shift
Pyrene		P6115 P130 P6114 (CASE)	P24 (SC) P10167 (STP)	345	378	Long excited-state lifetime Spectral shifts due to excimer emission
QSY 7		Q10193		560	none	Essentially nonfluorescent quencher Broad visible-wavelength absorption Efficient energy transfer acceptor from green and orange fluorophores
QSY 9		Q20131		562	none	Essentially nonfluorescent quencher Spectrally similar to QSY 7, but with enhanced water solubility Efficient energy-transfer acceptor from green and orange fluorophores
QSY 21		Q20132		661	none	Essentially nonfluorescent quencher Long-wavelength absorption An efficient energy transfer acceptor from red and near-infrared fluorophores
QSY 35		Q20133		475	none	Nonfluorescent quencher Spectrally similar to dabcyl An efficient energy transfer acceptor from blue and green fluorophores
Rhodamine 6G		C6127 C6128 C6157		525	555	Excited by the 514 nm spectral line of the Ar-ion laser Spectra intermediate between those of fluorescein and tetramethylrhodamine
Rhodamine Green dye		R6107 R6112 R6113 (X)		502	527	Photostable fluorescein substitute pH-insensitive fluorescence
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
2',4',5',7'-Tetrabromosulfonefluorescein		C6166		528	544	Eosin derivative useful for DAB photoconversion
2',4,7,7'-Tetrachlorofluorescein, succinimidyl ester (TET)		C20092		521	536	Succinimidyl ester derivative (6-TET, SE; C20092) is widely used for automated DNA sequencing
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 Succinimidyl ester derivative (6-TAMRA, SE; C6123) is widely used for automated DNA sequencing
Texas Red dye		T6134 (X) T20175 (X)	T353 (SC) T1905 (SC) T10125 (STP)	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
X-rhodamine	C6124 C6156	C6125 C6126 C1309	X491 (ITC)	580	605	Succinimidyl ester derivative (6-ROX, SE; C6126) is widely used for automated nucleic acid sequencing
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. Full spectra for many dyes are available from this web site. * COOH = carboxylic acid; SE = succinimidyl ester; (AA) = acetyl azide; (AH) = aryl halide; (C₅) = pentanoic acid; (CASE) = cysteic acid; succinimidyl ester; (DTA) = dichlorotriazine; (EX) = seven-atom spacer that is more hydrophilic than X; (ITC) = isothiocyanate; (SC) = sulfonyl chloride; (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.