6-JOE Phosphoramidite

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Additional ordering information

Telephone	1-800-990-8053
Fax	1-800-609-2943
Email	sales@aatbio.com
Quotation	Request
International	See distributors
Shipping	Standard overnight for United States, inquire for international

Physical properties

Molecular weight	972.89
Solvent	MeCN

Spectral properties

Extinction coefficient (cm ^-1 M ^-1)	75000¹
Excitation (nm)	520
Emission (nm)	545

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

Molecular weight

972.89

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

75000¹

Excitation (nm)

520

Emission (nm)

545

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-FAM, 6-HEX, 6-TET and 6-JOE, 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. AAT Bioquest offers 6-FAM, 6-HEX, 6-TET and 6-JOE phosphoramidites for effectively labeling oligos. AAT Bioquest offers 6-JOE Phosphoramidite to facilitate the labeling of oligos with JOE. Helix Fluor™ 6-JOE Phosphoramidite can be conveniently used to prepare the oligos that have essentially identical spectral and biological properties to the ones that are derived from 6-JOE, SE.

Calculators

Common stock solution preparation

Table 1. Volume of MeCN needed to reconstitute specific mass of 6-JOE 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	102.787 µL	513.933 µL	1.028 mL	5.139 mL	10.279 mL
5 mM	20.557 µL	102.787 µL	205.573 µL	1.028 mL	2.056 mL
10 mM	10.279 µL	51.393 µL	102.787 µL	513.933 µL	1.028 mL

Molarity calculator

Enter any two values (mass, volume, concentration) to calculate the third.

Mass (Calculate)		Molecular weight		Volume (Calculate)		Concentration (Calculate)		Moles
	/		=		x		=

Spectrum

Open in Advanced Spectrum Viewer

Spectral properties

Extinction coefficient (cm ^-1 M ^-1)	75000¹
Excitation (nm)	520
Emission (nm)	545

Product Family

Name	Excitation (nm)	Emission (nm)	Extinction coefficient (cm ^-1 M ^-1)	Correction Factor (280 nm)
6-JOE, SE [6-Carboxy-4',5'-dichloro-2',7'-dimethoxyfluorescein, succinimidyl ester] CAS#: 113394-23-3	520	545	75000¹	-
6-JOE azide	520	545	75000¹	-
6-JOE alkyne	520	545	75000¹	-
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-HEX phosphoramidite [5'-Hexachlorofluorescein phosphoramidite]	533	559	73000	0.15
6-JOE acid	520	545	75000¹	-

Images

Figure 1. Chemical structure for 6-JOE 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