Hexachloro-fluorescein (HEX) (absorbance maximum of 535 nm, emission maximum of 556 nm), a hexachlorinated version of the fluorescent dye fluorescein, can be used to label oligonucleotides at 5- or 3-end.  HEX can be used in real-time PCR, being used as a reporter moiety in TaqMan probes, Scorpion primers, and Molecular Beacons (1,2,3).   For the above applications, HEX is commonly paired with the dark quencher BHQ-1, as they exhibit good spectral overlap.    HEX labeled oligonucleotides (DNA) as hybridization probes are useful for various in vivo and in vitro research/diagnostic applications, and for structure-function studies of DNA, RNA, and protein-oligonucleotide complexes.  Oligonucleotides labeled with HEX at 5-end can be used to generate fluorescently-labeled PCR products, as primers for DNA sequencing, or for genetic analysis (AFLP or microsatellite).  If HEX is on the 3-end of the oligo, it cannot be used as a primer in PCR-based applications.


1. Livak, K.J., Flood, S.J.A., Marmaro, J., Giusti, W., Deetz, K. Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization.PCR Methods Appl. (1995), 4: 1-6.

2. Thelwell, N., Millington, S., Solinas, A., Booth, J., Brown, T. Mode of action and application of Scorpion primers to mutation detection.  Nucleic Acids Res. (2000), 28: 3752-3761.

 3. Tyagi, S., Kramer, F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. (1996), 14: 303-308.   

Product Information


Product Name:

HEX, Hexachlorofluorescein Oligonucleotide Labeling

Alternate Name:

Hexachloro Fluorescein


Fluorescent Dyes

Modification Code:


Chemical Formula:


Exact Mass:


Formula Weight:


Absorption λmax:

535 nm

Emission (nm):

556 nm

Extinction Coefficient, ε(λ):



Bio-Synthesis Inc. Oligo Structure



Delivery Format:


Shipping Conditions:

Room Temperature

Storage Conditions:

-20°C To -70°C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Dried DNA (when kept at -20°C) in a nuclease-free environment should be stable for years.