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Hex-5' (Hexachloro-Fluorescein)


Code : [5-Hex]

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picture of Hex-5' (Hexachloro-Fluorescein)

Modification : Hex-5'

Catalog Reference Number
Modification Code
5 Prime
3 Prime
Molecular Weight (mw)
Extinction Coeficient (ec)
Technical Info (pdf)
Absorbance MAX
Emission MAX
Absorbance EC

Fluorescent Dyes

Catalog NoScalePrice
26-6432-0550 nmol$115.00
26-6432-02200 nmol$115.00
26-6432-011 umol$185.00
26-6432-032 umol$235.00
26-6432-1010 umol$708.00
26-6432-1515 umol$885.00
Discounts are available for Hex-5'!
Modification* Discount Price Structure
1 site/order List price
2 sites/order 10% discount
3 sites/order 20% discount
4 sites/order 30% discount
5-9 sites/order 50% discount
10+ sites/order 60% discount
*Exceptions apply

Click here for a list of fluorophores.

Hexachloro-fluorescein (HEX) is hexachlorinated version of the fluorescent dye fluorescein, and is used for labeling oligonucleotides at either the 5' or 3' end. HEX has an absorbance maximum of 535 nm and an emission maximum of 556 nm. HEX can be used in real-time PCR applications as a reporter moiety in TaqMan probes (1), Scorpion primers (2) and Molecular Beacons (3). For such probes, HEX is most commonly paired with the dark quencher BHQ-1, as the two have good spectral overlap.

HEX also can be used to label DNA oligos for use as hybridization probes in a variety of in vivo and in vitro research or diagnostic applications, as well as for structure-function studies of DNA, RNA, and protein-oligonucleotide complexes. Oligos labeled with HEX at the 5' end can be used as PCR and DNA sequencing primers to generate fluorescently-labeled PCR, sequencing or genetic analysis (AFLP or microsatellite) products. NOTE: If HEX is on the 3' end of the oligo, it cannot be used as a primer in PCR-based applications.

Applied Biosystems Proprietary Dyes & Possible Substitutions



Absorbance max (nm)

Emission max (nm)

VIC Pink Red 538 554
Cal Orange 560 Pink Red 537 558
HEX Pink Red 535 556
NED Red Orange 546 575
Cy3 Red Orange 550 570
PET Red Orange 558 595
Cy3.5 Red 588 604
ROX Red 575 602
Texas Red Red 583 603

Click here for a list of fluorophores.

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.
- Hex-5' (Hexachloro-Fluorescein)

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