Yakima Yellow® Phosphoramidite

3-(5,6,4',7'-tetrachloro-5'-methyl-3',6'-dipivaloylfluorescein-2-yl)-propanamidohexyl-1-O-(2-cyanoethyl)-(N,N-diisopropyl)-phosphoramidite

Product Specifications

Formula:
C49H60Cl4N3O10P
M.W.:
1023.81
F.W.:
718.33
CAS Number:
502485-39-4
To Retrieve a Catalog Number, Select a Pack Size and Format:

Description

Glen Research’s agreement with ELITechGroup, formerly Epoch Biosciences, allows us to offer several of their proprietary products designed for the synthesis of novel DNA probes. We are pleased to offer products based on ELITechGroup’s Redmond Red®, Yakima Yellow® and AquaPhluor® 593 fluorophores and Eclipse® non-fluorescent quencher. Under our agreement we also supply PPG, a modified nucleoside, and 5’-Aldehyde-Modifier C2 Phosphoramidite. The fluorescent dyes, Yakima Yellow, Redmond Red and AquaPhluor 593, are available as phosphoramidites and supports. Yakima Yellow has an absorbance maximum at 530 nm and emission maximum at 549 nm, Redmond Red’s absorbance and emission maxima are at 579 nm and 595 nm, respectively, and AquaPhluor 593 has an absorbance maximum at 593 nm and emission maximum at 613 nm. The fluorescein alternative, Gig Harbor Green, has been discontinued. The Eclipse quencher from ELITechGroup solves most of the problems inherent in the synthesis of molecular beacon and FRET probes. The Eclipse molecule is highly stable and can be used safely in all common oligo deprotection schemes. The absorbance maximum for Eclipse Quencher is at 522 nm, compared to 479 nm for dabcyl. In addition, the structure of the Eclipse Quencher is substantially more electron deficient than that of dabcyl and this leads to better quenching over a wider range of dyes, especially those with emission maxima at longer wavelengths (red shifted) such as Redmond Red and Cyanine 5. In addition, with an absorption range from 390 nm to 625 nm, the Eclipse Quencher is capable of effective performance in a wide range of colored FRET probes.

The spectral characteristics of this dye is detailed here.

Details

Usage

  • Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
  • Deprotection: Use ammonium hydroxide and deprotect as required by nucleobases. When using AMA, a small amount of a non-fluorescent impurity will be formed. To eliminate this impurity, first deprotect with ammonium hydroxide for 30 minutes at room temperature, add an equal volume of 40% methylamine and then complete the deprotection as required by the nucleobases - e.g. 10 minutes at 65°C or 2 hours at room temperature for standard bases.
Specifications
Diluent Anhydrous Acetonitrile
Storage Freezer storage, -10 to -30°C, dry

Intellectual Property

Yakima Yellow®, Redmond Red®, Eclipse® and MGB Eclipse® are registered Trademarks of ELITechGroup. Product is made and sold under license from ELITechGroup.

Dilution/Coupling Data

The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.

ABI 392/394

Catalog # Pack Size Grams/Pack 0.1M Dil. (mL) Approximate Number of Additions
LV40 LV200 40nm 0.2μm 1μm 10μm
10-5921-02 0.25 g .25grams 2.44 68 40.8 25.5 18.55 13.6 3.4
10-5921-90 100 µmol .102grams 1 20 12 7.5 5.45 4 1
10-5921-95 50 µmol .051grams 0.5 3.33 2 1.25 0.91 0.67 0.17

Expedite

Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-5921-02 0.25 g .25grams 3.64 0.07 66.4 41.5 30.18 4.15
10-5921-90 100 µmol .102grams 1.5 0.07 23.6 14.75 10.73 1.48
10-5921-95 50 µmol .051grams 0.75 0.07 8.6 5.38 3.91 0.54



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