6-HEX phosphoramidite [5'-Hexachlorofluorescein phosphoramidite]

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Physical properties

Molecular weight	1050.61
Solvent	MeCN

Spectral properties

Correction Factor (280 nm)	0.15
Extinction coefficient (cm ^-1 M ^-1)	73000
Excitation (nm)	533
Emission (nm)	559

Storage, safety and handling

H-phrase	H303, H313, H333
Hazard symbol	XN
Intended use	Research Use Only (RUO)
R-phrase	R20, R21, R22
Storage	Freeze (< -15 °C); Minimize light exposure
UNSPSC	12171501

Overview SDS Protocol

CAS

1360547-55-2

Molecular weight

1050.61

Correction Factor (280 nm)

0.15

Extinction coefficient (cm ^-1 M ^-1)

73000

Excitation (nm)

533

Emission (nm)

559

There are several ways of labeling an oligonucleotide with fluorescein. The choice of label is diversified further, depending on the spectral requirements. 5'-fluorescein-CE phosphoramidite, derived from the single isomer 6-carboxyfluorescein, 5'-hexachlorofluorescein-CE phosphoramidite (HEX) and 5'-tetrachlorofluorescein-CE phosphoramidite (TET) can all be used to efficiently label an oligonucleotide at the 5'-end. Labeling the 3'-end of an oligo with fluorescein can be achieved using 3'-Fluorescein CPGs. Standard cleavage and deprotection with ammonium hydroxide liberates the fluorescein-labeled oligo when using any of these supports.

Calculators

Common stock solution preparation

Table 1. Volume of MeCN needed to reconstitute specific mass of 6-HEX phosphoramidite [5'-Hexachlorofluorescein phosphoramidite] to given concentration. Note that volume is only for preparing stock solution. Refer to sample experimental protocol for appropriate experimental/physiological buffers.

	0.1 mg	0.5 mg	1 mg	5 mg	10 mg
1 mM	95.183 µL	475.914 µL	951.828 µL	4.759 mL	9.518 mL
5 mM	19.037 µL	95.183 µL	190.366 µL	951.828 µL	1.904 mL
10 mM	9.518 µL	47.591 µL	95.183 µL	475.914 µL	951.828 µL

Molarity calculator

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Mass (Calculate)		Molecular weight		Volume (Calculate)		Concentration (Calculate)		Moles
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Spectrum

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Spectral properties

Correction Factor (280 nm)	0.15
Extinction coefficient (cm ^-1 M ^-1)	73000
Excitation (nm)	533
Emission (nm)	559

Product Family

Name	Excitation (nm)	Emission (nm)	Extinction coefficient (cm ^-1 M ^-1)	Correction Factor (280 nm)
6-HEX, SE [6-Carboxy-2',4,4',5',7,7'-hexachlorofluorescein, succinimidyl ester] Single Isomer	533	559	73000	0.15
6-HEX azide	533	559	73000	0.15
6-HEX alkyne	533	559	73000	0.15
6-FAM phosphoramidite [5'-Fluorescein phosphoramidite] CAS 204697-37-0	493	517	83000	0.178
6-Fluorescein phosphoramidite	498	517	80000¹	0.35
6-TET phosphoramidite [5'-Tetrachlorofluorescein phosphoramidite] CAS#: 877049-90-6	521	542	73000	0.13
6-JOE Phosphoramidite	520	545	75000¹	-
HEX-dT Phosphoramidite	533	559	73000	0.15
6-HEX acid	533	559	73000	0.15
6-VIC phosphoramidite	526	543	-	-
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Images

Figure 1. Chemical structure for 6-HEX phosphoramidite [5'-Hexachlorofluorescein phosphoramidite]

References

View all 13 references: Citation Explorer

Sequence-specific, self-reporting hairpin inversion probes
Authors: Browne KA., undefined
Journal: J Am Chem Soc (2005): 1989

Modified oligonucleotides containing lithocholic acid in their backbones: their enhanced cellular uptake and their mimicking of hairpin structures
Authors: Kim SJ, Bang EK, Kwon HJ, Shim JS, Kim BH.
Journal: Chembiochem (2004): 1517

Synthesis of HyBeacons and dual-labelled probes containing 2'-fluorescent groups for use in genetic analysis
Authors: Dobson N, McDowell DG, French DJ, Brown LJ, Mellor JM, Brown T.
Journal: Chem Commun (Camb) (2003): 1234

Reduced aggregation and improved specificity of G-rich oligodeoxyribonucleotides containing pyrazolo[3,4-d]pyrimidine guanine bases
Authors: Kutyavin IV, Lokhov SG, Afonina IA, Dempcy R, Gall AA, Gorn VV, Lukhtanov E, Metcalf M, Mills A, Reed MW, S and ers S, Shishkina I, Vermeulen NM.
Journal: Nucleic Acids Res (2002): 4952

Diels--Alder bioconjugation of diene-modified oligonucleotides
Authors: Hill KW, Taunton-Rigby J, Carter JD, Kropp E, Vagle K, Pieken W, McGee DP, Husar GM, Leuck M, Anziano DJ, Sebesta DP.
Journal: J Org Chem (2001): 5352

Recovery of an oligonucleotide using silver ions immobilized onto paramagnetic particles
Authors: Ramirez-Vick JE, Garcia AA, Lee J.
Journal: Prep Biochem Biotechnol (1998): 243

Simultaneous detection of several oligonucleotides by time-resolved fluorometry: the use of a mixture of categorized microparticles in a sandwich type mixed-phase hybridization assay
Authors: Hakala H, Virta P, Salo H, Lonnberg H.
Journal: Nucleic Acids Res (1998): 5581

Synthesis and characterization of a new 5-thiol-protected deoxyuridine phosphoramidite for site-specific modification of DNA
Authors: Meyer KL, Hanna MM.
Journal: Bioconjug Chem (1996): 401

Synthesis and characterisation of fluorescent oligonucleotides. Effect of internal labelling on protein recognition
Authors: Hagmar P, Bailey M, Tong G, Haralambidis J, Sawyer WH, Davidson BE.
Journal: Biochim Biophys Acta (1995): 259

Characterization of endonucleolytic activity of HIV-1 integrase using a fluorogenic substrate
Authors: Lee SP, Censullo ML, Kim HG, Knutson JR, Han MK.
Journal: Anal Biochem (1995): 295