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FAM (fluorescein) phosphoramidite 6-isomer is specifically designed for incorporation at the 5′-end of oligonucleotides, which is essential for many biochemical assays and applications. It is primarily utilized for labeling oligonucleotides, enhancing their visibility in various assays such as PCR, sequencing and hybridization studies. It is commonly employed in real-time PCR assays where fluorescent signals are monitored during amplification. The incorporation of FAM at the 5′-end allows for efficient monitoring of the reaction progress through fluorescence.

FAM emits fluorescence with a maximal emission wavelength around 517 nm, which is ideal for various detection methods. It can be quenched by agents like DusQ 1 or DABCYL, allowing for applications in assays that require precise control over fluorescence signals.

Internal sequence additions can be achieved using modified nucleotides such as FAM-dT phosphoramidite, allowing for flexible design of probes with multiple fluorescent tags while maintaining effective spacing. However, it is essential to include spacers between the labels to prevent self-quenching of fluorescence signals, which can occur due to close proximity.

The dye soluble in common organic solvents such as acetonitrile, DCM, DMF, DMSO. Once conjugated to biomolecules, the resulting FAM conjugates can be used in aqueous applications.