5'(6)-FAM Chemical Properties

Boiling point:

850.6±65.0 °C(Predicted)

storage temp. 

-20°C

solubility 

acetonitrile: soluble 0.1M, clear, colorless to faintly yellow (liquid)

pka

14.56±0.20(Predicted)

color 

solid white to off-white

Appearance

off-white solid

InChIKey

MGPYJVWEJNTXLC-UHFFFAOYSA-N

SMILES

C12(C3=C(C=C(OC(=O)C(C)(C)C)C=C3)OC3=C1C=CC(OC(=O)C(C)(C)C)=C3)C1=C(C=CC(C(=O)NCCCCCCOP(N(C(C)C)C(C)C)OCCC#N)=C1)C(=O)O2

Safety Information

WGK Germany 

3

5'(6)-FAM Usage And Synthesis

Description

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.

Chemical Properties

5'-Fluorescein phosphoramidate is soluble in common organic solvents such as acetonitrile, DCM, DMF, and DMSO. After conjugation with biomolecules, the resulting FAM conjugates can be used in aqueous applications.

Uses

6-Fluorescein phosphoramidite is a potent fluorescent dye. 6-Fluorescein phosphoramidite can be used to label oligonucleotides[1].

References

[1] Lietard J, et al. Sequence-dependent quenching of fluorescein fluorescence on single-stranded and double-stranded DNA. RSC Adv. 2022 Feb 16;12(9):5629-5637. DOI:10.1039/d2ra00534d

Abs/Em Maxima

492/517 nm

Fluoresene quantum yield

0.93

Extinction Coefficient

74000

CF260

0.22

CF280

0.17

5'(6)-FAM(204697-37-0)Related Product Information

• 6-TET phosphoramidite [5'-Tetrachlorofluorescein phosphoramidite]
• Propanoic acid, 2,2-dimethyl-, 1,1'-[6-[10-[bis(1-methylethyl)amino]-13-cyano-1-oxo-9,11-dioxa-2-aza-10-phosphatridec-1-yl]-2',4,4',5',7,7'-hexachloro-3-oxospiro[isobenzofuran-1(3H),9'-[9H]xanthene]-3',6'-diyl] ester
• FLUORESCEIN DIPROPIONATE
• 5'(6)-FAM
• N-(6-HYDROXYHEXYL)-6-CARBOXAMIDOFLUORESCEIN DIPIVALATE