Table 1.12 Amine-reactive, ultraviolet light–excitable fluorophores for labeling proteins and nucleic acids.

Fluorophore Abs * Em * Amine-Reactive Dyes Protein and Nucleic Acid Labeling Kits Notes
Alexa Fluor 350 346 442 A10168 (SE) A20180 (Ab)
A10170 (P)
Z25000 (Z)
Z25100 (Z)
Z25200 (Z)
Z25300 (Z)
Z25400 (Z)
  • Higher fluorescence per attached dye than AMCA
  • Protein conjugates emit at slightly shorter wavelengths than AMCA or AMCA-X
Alexa Fluor 405 402 421 A30000 (SE)
A30100 (SE)
Z25013 (Z)
Z25113 (Z)
Z25213 (Z)
Z25313 (Z)
  • Cascade Blue derivative containing a spacer between the fluorophore and the reactive SE
  • Near-perfect match to the 405 nm violet diode laser
Alexa Fluor 430 433 539 A10169 (SE) A10171 (P)
Z25001 (Z)
Z25301 (Z)
  • Extremely large Stokes shift
  • Fills spectral gap between green- and yellow-fluorescent dyes
AMCA-X 353 442 A6118 (SE)  
  • Widely used blue-fluorescent labeling dye
  • Compact structure
Bimane 380 458 B30250 (COOH)  
  • Blue-fluorescent dye
  • Small size
Cascade Blue 400 420 C2284 (AA)  
  • Resistant to quenching upon protein conjugation
  • Trisulfonated pyrene
Dialkylaminocoumarin 375
470 (1)
475 (2)
D126 (COOH)
D1421 (COOH)
D374 (SE)
D1412 (SE)
D10166 (ITC)
  • Longer-wavelength alternatives to AMCA
Hydroxycoumarin 385
445 (3)
455 (4)
H185 (COOH)
H1428 (COOH)
H1193 (SE)
  • pH-sensitive fluorescence
  • Compact structure
Marina Blue 365 460 M10165 (SE)  
  • Optimal for 365 nm excitation sources
Methoxycoumarin 358 410 M1420MP (COOH)
M1410 (SE)
  • pH-insensitive fluorescence
  • Compact structure
Pacific Blue 410 455 P10163 (SE) A10478 (APEX)
P30013 (Ab)
P30012 (P)
Z25041 (Z)
Z25341 (Z)
  • Longer-wavelength alternative to the Alexa Fluor 350 and AMCA-X dyes
  • Excited with the 405 nm violet diode laser
Pacific Orange 400 551 P30253 (SE) P30014 (Ab)
P30016 (P)
Z25256 (Z)
Z25257 (Z)
  • Excited with the 405 nm violet diode laser
  • Compatible with the Pacific Blue dye for two-color analysis using the blue diode laser

* The absorption (Abs) and fluorescence emission (Em) maxima, in nm, listed in this table are for the goat anti–mouse IgG antibody or dextran conjugates in aqueous buffer.

(1) Spectral maxima for D374.
(2) Spectral maxima for D1412.
(3) Spectral maxima for H1193.
(4) Spectral maxima for 7-hydroxy-4-methylcoumarin-3-acetic acid, succinimidyl ester.

(AA) = Acetyl azide.
(Ab) = Antibody Labeling Kit (Kits for Labeling Proteins and Nucleic Acids—Section 1.2).
(APEX) = APEX Antibody Labeling Kit (Kits for Labeling Proteins and Nucleic Acids—Section 1.2).
(COOH) = Carboxylic acid.
(ITC) = Isothiocyanate.
(P) = Easy-to-Use Protein Labeling Kit (Kits for Labeling Proteins and Nucleic Acids—Section 1.2).
(SE) = Succinimidyl ester.
(Z) = Zenon Antibody Labeling Kit (Zenon Technology: Versatile Reagents for Immunolabeling—Section 7.3).