HEX phosphoramidite, 6-isomer

Cat. # Quantity Price Lead time
CB260 100 mg –   in stock
DB260 250 mg $360.00 in stock
FB260 1 g $760.00 in stock
GB260 5 g $3490.00 10 days
HB260 10 g please inquire 21 days

HEX phosphoramidite for oligonucleotide synthesis, pure 6-isomer.

HEX (hexachlorofluorescein) is a fluorescein derivative with emission in the yellow spectrum range (absorption maximum at 533 nm, emission maximum at 549 nm).

HEX phosphoramidite is used for synthesis of fluorescent-labeled primers and hybridization probes such as TaqMan, Molecular Beacon, and Scorpion for qPCR. HEX is most effectively quenched by non-fluorescent DusQ1 dark quencher because of significant overlapping of their spectra (convenient for use with DusQ1 CPG 500 solid support with a pore size of 500 Å). Many automated sequencers based on capillary gel electrophoresis have a detection channel for HEX. Therefore, this phosphoramidite is commonly used for synthesis of 5’-labeled oligonucleotides for fragment analysis, particularly for microsatellite analysis, when microsatellite loci are amplified using a fluorescent-labeled forward primer and a non-labeled reverse primer.


Coupling: 3 min.

Deprotection: standard conditions using 25% ammonium; deprotection time depends on oligonucleotide composition and nucleobase protecting groups (deprotection for 17 h at 55 °С removes all protecting groups from standard nucleobases). AMA (solution of concentrated aqueous ammonium/40% aqueous methylamine 1:1 v/v) can be used with ~5% of non-fluorescent side product forming. To avoid formation of the side product, start deprotection with ammonium hydroxide (30 min at room temperature), then add an equal volume of 40% aqueous methylamine and continue deprotection as required with AMA (e.g. 10 min at 65 °C).

Absorption and emission spectra of HEX

Absorption and emission spectra of HEX

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General properties

Appearance: off white solid
Molecular weight: 1050.61
CAS number: 1360547-55-2
Molecular formula: C46H52N3Cl6O10P
Solubility: Good solubility in acetonitrile and DCM.
Quality control: NMR 1H and 31P, HPLC-MS
Storage conditions: Storage: 12 months after receival at -20°C in the dark. Transportation: at room temperature for up to 3 weeks. Avoid prolonged exposure to light. Desiccate.
MSDS: Download
Product specifications

Spectral properties

Excitation/absorption maximum, nm: 533
ε, L⋅mol−1⋅cm−1: 87770
Emission maximum, nm: 549
Fluorescence quantum yield: 0.57
CF260: 0.30
CF280: 0.13

Oligo synthesis details

Diluent: anhydrous acetonitrile (prepare a 0.1 М solution, storage 1 week).
Coupling conditions: standard coupling, identical to normal nucleobases
Deprotection conditions: identical to protected nucleobases
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