Conjugates prepared with the thiol-reactive Alexa Fluor 647® C2 maleimide are spectrally similar to the Cy5 dye, resulting in an optimal match to optical filters for the Cy5 dye. Total fluorescence of secondary antibody conjugates of Alexa Fluor® 647 dye, however, is significantly higher than that of Cy5 conjugates. Unlike the Cy5 dye, Alexa Fluor® 647 dye has very little change in absorption of fluorescence spectra when conjugated to most porteins, oligonucleotides, or nucleic acids, yielding greater total fluorescence at the same degree of substitution.
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