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.

Usage

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

Customers also purchased with this product

TET phosphoramidite, 6-isomer

TET phosphoramidite for synthesis of 5’-labeled oligonucleotides.

Alkyne Amidite, hydroxyprolinol

Acetylenic amidite for the incorporation of acetylene groups into oligos.

DusQ2 CPG 500

Controlled pore glass (CPG) 500 modified support for the synthesis of oligonucleotides with DusQ2 quencher at the 3’ end. Compatible with standard deblocking conditions.
Add this product to your cart and
get free express delivery

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
Your item has been added. View your cart or proceed to checkout
The count of items is incorrect.