Enhanced Diagnostic Tools
The excitation and emission spectra of the Alexa Fluor series cover the visible spectrum and extend into the infrared. The individual members of the family are numbered according roughly to their excitation maxima (in nm).
Alexa Fluor dyes are synthesized through sulfonation of coumarin, rhodamine, xanthene(such as fluorescein), and cyanine dyes. Sulfonation makes Alexa Fluor dyes negatively charged and hydrophilic. Alexa Fluor dyes are generally more stable, brighter, and less pH-sensitive than common dyes (e.g. fluorescein, rhodamine) of comparable excitation and emission, and to some extent the newer cyanine series. However, they are also more expensive. They are patented by Invitrogen (which acquired the company that developed the Alexa dyes, Molecular Probes) and thus are priced higher than the common dyes that are available from multiple manufacturers.
Similar alternatives include the DyLight Fluors from Pierce (Thermo Fisher Scientific), and the Atto series from Atto-Tec and sold by Sigma-Aldrich
Tetramethylrhodamine, Cy3 dye
Lissamine rhodamine B dye, Rhodamine Red dye
Texas Red dye, Cy3.5 dye
Cy5 dye, allophycocyanin (APC)
Comparison with other dyes
The Alexa series dyes are less pH-sensitive and more photostable than the original dyes (fluorescein, rhodamine, etc.) from which they were synthesized.
However, brightness comparisons are not presently available. Brightness is commonly measured as a product of extinction coefficient (absorption efficiency) and quantum yield (emission efficiency)  While extinction coefficients are known (see the table above), the quantum yields of the Alexas have not been published by Molecular Probes.
In one case, a third party has compared one Alexa with another commonly used dye. This was a comparison of Cy5 and its Alexa with similar wavelength, Alexa 647, with the dyes conjugated to DNA.  This study found that Cy5 is brighter, but less photostable than Alexa 647.
Therefore presently it is difficult to quantitatively choose the best dye for a particular application and in many cases empirical testing is in order.
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