Calculator
6-JOE Phosphoramidite
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
Product family
| Name | Excitation (nm) | Emission (nm) | Extinction coefficient (cm -1 M -1) | Correction Factor (280 nm) |
| 6-FAM phosphoramidite [5'-Fluorescein phosphoramidite] *CAS 204697-37-0* | 493 | 517 | 83000 | 0.178 |
| 6-Fluorescein phosphoramidite | 498 | 517 | 800001 | 0.35 |
| 6-HEX phosphoramidite [5'-Hexachlorofluorescein phosphoramidite] | 533 | 559 | 73000 | 0.15 |
| 6-JOE acid | 520 | 545 | 750001 | - |
| 6-JOE alkyne | 520 | 545 | 750001 | - |
| 6-JOE azide | 520 | 545 | 750001 | - |
| 6-JOE, SE [6-Carboxy-4',5'-dichloro-2',7'-dimethoxyfluorescein, succinimidyl ester] *CAS#: 113394-23-3* | 520 | 545 | 750001 | - |
| 6-TET phosphoramidite [5'-Tetrachlorofluorescein phosphoramidite] *CAS#: 877049-90-6* | 521 | 542 | 73000 | 0.13 |
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
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
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
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
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
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
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