Oligo Synthesis : CEPs
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Cyanine 5 Phosphoramidite
Cyanine 5 Phosphoramidite
Glen Research
| Catalogue No. | Description | Pack Size | Price | Qty |
|
|---|---|---|---|---|---|
| 10-5915-02 | Cyanine 5 Phosphoramidite | 0.25g | £740.00£703.00Offer until : 31-Mar-2021Offer Code : GLEN5View Offer | Quantity | Add to Order |
| 10-5915-90 | Cyanine 5 Phosphoramidite | 100µmoles | £278.00£285.00Offer until : 31-Mar-2021Offer Code : GLEN5View Offer | Quantity | Add to Order |
| 10-5915-95 | Cyanine 5 Phosphoramidite | 50µmoles | £164.00£155.80Offer until : 31-Mar-2021Offer Code : GLEN5View Offer | Quantity | Add to Order |
Related products
Cyanine 5 Phosphoramidite
Cyanine 5 Phosphoramidite
Glen Research
| Cyanine 5 Phosphoramidite |
Catalog Number: 10-5915-xx
Description: Cyanine 5 Phosphoramidite
| 1-[3-(4-monomethoxytrityloxy)propyl]-1"-[3-[(2-cyanoethyl)-(N,N-diisopropylphosphoramidityl]propyl]-3,3,3",3"-tetramethylindodicarbocyanine chloride | ||
| Formula: C60H72N4O4PCl | M.W.: 979.68 | F.W.: 533.63 |
Diluent: Anhydrous Acetonitrile |
| Coupling: 3 minute coupling time recommended.The use of UltraMILD monomers are preferred. (Catalog Numbers: dA: 10-1601-xx, dC: 10-1015-xx, dG: 10-1621-xx, dT: 10-1030-xx).To avoid any exchange of the iPr-Pac group on the dG with acetyl, use the UltraMild Cap Mix A (40-4210-xx/ 40-4212-xx).0.02M Iodine for oxidation is recommended. |
| Deprotection: If UltraMILD reagents were used, deprotect in 0.05M Potassium Carbonate in Methanol for 4 hours at Room Temperature OR for 2 hours at Room Temperature in 30% Ammonium Hydroxide. If standard bases were used, deprotection in Ammonium Hydroxide at Room Temperature for 24-36 hours will give acceptable yields.However, the oligonucleotide will require a reverse phase purification, e.g., Poly Pak. Technical Bulletin |
| Storage: Freezer storage, -10 to -30°C, dry |
| Stability in Solution: 24 hours |
CYANINE LABELLINGTwo cyanine derivatives, Cyanine 3 and Cyanine 5, which differ in structure simply bythe number of carbons in the conjugated poly-ene linkage, are joined by theclosely related analogues, Cyanine 3.5 and Cyanine 5.5, and are available asphosphoramidites. Cyanine dyes are normally added once at the 5’-terminus and the MMTgroup should be removed on the synthesizer. The absorbance of the MMT cation(yellow) is noticeably different from the DMT cation (orange), and so,absorbance-based trityl monitors will detect it incorrectly as a low coupling.On the other hand, conductivity detectors will interpret the release morecorrectly. Cyanine dyes have also been used successfully adjacent to the 3’-terminusas long as 0.02M iodine oxidizer is used during the remainder of thesynthesis. Deprotection of oligos containing Cyanine dyes may be carried out with ammoniumhydroxide at room temperature, regardless of the base protecting groups on themonomers used. If there is a need to use ammonium hydroxide at elevatedtemperature, Cyanine 3 and Cyanine 3.5 are more stable than Cyanine 5 and Cyanine 5.5. However, it isalways prudent to use monomers with base labile protecting groups to limit theexposure time to 2 hours or less at 55°C. |
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Cyanine 5 Phosphoramidite
Cyanine 5 Phosphoramidite
Glen Research
Material Safety Data Sheet
| Glen Report 8.2: 5" LABELLING - FLUORESCEIN AND CYANINE DYES, BIOTIN |
| Glen Report 21.2: Deprotection - Volume 3 - Dye-Containing Oligonucleotides |
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Cyanine 5 Phosphoramidite
Cyanine 5 Phosphoramidite
Glen Research
Frequently Asked Technical Question
QUESTION: What are the relative extinction coefficients of 5"-Fluorescein, Hex and Tet etc.. at 260 nm and their Lambda max?
RESPONSE:Please see http://www.glenresearch.com/Technical/Extinctions.html
REFERENCE(S):Oligonucleotide Properties Calculator;http://www.basic.northwestern.edu/biotools/oligocalc.html
QUESTION: What are the relative extinction coefficients of various dyes?
RESPONSE:Please see http://www.glenres.com/Technical/Extinctions.html#dyes
QUESTION: Does AMA or methylamine cause any degradation to fluorescein or fluorescein-type dyes such as FAM or FITC?
RESPONSE:Response:While AMA (Ammonium hydroxide/40% Methylamine 1:1 v/v)is considered compatible with fluorescein, the use of methylamine when deprotecting a Fluorescein-labeled oligo does lead to a small amount of degradation, which is characterized by a the appearance of a late-eluting peak by RP HPLC that shows no visible fluorescein absorbance. With standard deprotection conditions (AMA 10 minutes at 65 C) the amount of degradation is approximately 5%.The impurity is not detected with AMA at RT for 2 hours.
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Cyanine 5 Phosphoramidite
Cyanine 5 Phosphoramidite
Glen Research
DILUTION/COUPLING DATA
The table below shows pack size data and, for solutions, dilutions and approximate couplings based on normal priming procedures. Please link for more detailed usage information with the various synthesizers.
| ABI 392/394 | |||||||||
| Cat.No. | PackSize | Grams/Pack | 0.1M Dil.(mL) | LV40 | LV200 | 40nm | 0.2µm | 1µm | 10µm |
| Approximate Number of Additions | |||||||||
| 10-5915-02 | 0.25grams | .25grams | 2.55 | 71.67 | 43 | 26.88 | 19.55 | 14.33 | 3.58 |
| 10-5915-90 | 100µmoles | .098grams | 1 | 20 | 12 | 7.5 | 5.45 | 4 | 1 |
| 10-5915-95 | 50µmoles | .049grams | .5 | 3.33 | 2 | 1.25 | .91 | .67 | .17 |
| Expedite | |||||||||
| Cat.No. | PackSize | Grams/Pack | Dilution(mL) | Molarity | 50nm | 0.2µm | 1µm | 15µm | |
| Approximate Number of Additions | |||||||||
| 10-5915-02 | 0.25grams | .25grams | 3.81 | .07 | 69.8 | 43.63 | 31.73 | 4.36 | |
| 10-5915-90 | 100µmoles | .098grams | 1.5 | .07 | 23.6 | 14.75 | 10.73 | 1.48 | |
| 10-5915-95 | 50µmoles | .049grams | .75 | .07 | 8.6 | 5.38 | 3.91 | .54 | |
| Beckman | |||||||||
| Cat.No. | PackSize | Grams/Pack | Dilution(mL) | Molarity | 30nm | 200nm | 1000nm | ||
| Approximate Number of Additions | |||||||||
| 10-5915-02 | 0.25grams | .25grams | 3.81 | .07 | 71.4 | 44.63 | 32.45 | ||
| 10-5915-90 | 100µmoles | .098grams | 1.5 | .07 | 25.2 | 15.75 | 11.45 | ||
| 10-5915-95 | 50µmoles | .049grams | .75 | .07 | 10.2 | 6.38 | 4.64 | ||
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