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Difference between FITC and 6-FAM labeled oligo

Difference between FITC and 6-FAM

6-FAM and FITC labeled oligo have similar spectral properties. 6-carboxyfluorescein also known as 6-FAM is a single isomer.  Fluorescein-5,6-isothiocyanate, is a mix isomers. They are derivatives of the fluorescent dye fluorescein. FITC has a isothiocyanate reactive group (-N=C=S) at one of two hydrogen atoms on the bottom ring of the structure below.  It is reactive toward primary amine to form a urea linkage. 6-FAM is often used for oligo labeling. This dye can be incorporate at time of synthesis or conjugate post-synthetically. The chemistry is more robust and result in better yield. Study has shown that 6-FAM is less susceptible to photobleaching.