HEX phosphoramidite, 6-isomer

Oligonucleotide synthesis HEX (Hexachlorofluorescein) Phosphoramidites

Cat. #	Quantity	Price	Lead time
CB260 / Easily soluble lyophilised form in 6 mL septum	100 mg	–	in stock
DB260 / Easily soluble lyophilised form in 6 mL septum	250 mg	$272	in stock
FB260 / Easily soluble lyophilised form in 20 mL septum	1 g	$575	in stock
GB260	5 g	$2640	in stock
HB260	10 g	please inquire	in stock

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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 DusQ 1 dark quencher because of significant overlapping of their spectra (convenient for use with DusQ 1 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).

Structure of HEX phosphoramidite, 6-isomer

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Absorption and emission spectra of HEX

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 HPLC-MS (95+%)
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

This Product is offered and sold for research purposes only. It has not been tested for safety and efficacy in food, drug, medical device, cosmetic, commercial or any other use. Supply does not express or imply authorization to use for any other purpose, including, without limitation, in vitro diagnostic purposes, in the manufacture of food or pharmaceutical products, in medical devices or in cosmetic products.