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Catalog Number: 10-5914-xx
Description: Cy3.5™ Phosphoramidite
| 1-[3-(4-monomethoxytrityloxy)propyl]-1'-[3-[(2-cyanoethyl)- (N,N-diisopropyl)phosphoramidityl]propyl]-3,3,3',3'-tetramethyl- 4,5-benzindocarbocyanine chloride | ||
| Formula: [C66H74N4O4P]+Cl- | M.W.: 1053.76 | F.W.: 607.70 |
Diluent: Anhydrous Acetonitrile |
| Coupling: 3 minute coupling time recommended. Use 0.02M Iodine to avoid degradation of the cyanine dye. |
| Deprotection: If dmf-dG is used during synthesis, deprotect in Ammonium Hydroxide for 2 hours at 65 °C; with ibu-dG, deprotect for 24-36 hours at room temperature. Note Cy3.5 is compatible with UltraFast deprotection (AMA 10 minutes at 65 °C) if Ac-dC was used. Technical Bulletin |
| Storage: Freezer storage, -10 to -30°C, dry |
| Stability in Solution: 2-3 days |
| Please Note: This material is subject to proprietary rights of GE Healthcare Bio-Sciences Corp. and/or Carnegie Mellon University and is made and sold under license from GE Healthcare Bio-Sciences Corp. under the following patents: US Patent No. 5,556,959 and 5,808,044, Patent Number DE3943862 and other pending patent applications. This product is licensed for sale only for research. It is NOT licensed for any other use. There is no implied license hereunder for any commercial use. Cy and CyDye are trademarks of GE Healthcare Limited. |
| Catalog Information | Material Safety Data Sheet |
Literature Highlights
| Glen Report 21.2: Deprotection - Volume 3 - Dye-Containing Oligonucleotides |
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.
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. | Pack Size | Grams/ Pack | 0.1M Dil. (mL) | LV40 | LV200 | 40nm | 0.2µm | 1µm | 10µm |
| Approximate Number of Additions | |||||||||
| 10-5914-02 | 0.25grams | .25grams | 2.37 | 65.67 | 39.4 | 24.63 | 17.91 | 13.13 | 3.28 |
| 10-5914-90 | 100µmoles | .105grams | 1 | 20 | 12 | 7.5 | 5.45 | 4 | 1 |
| 10-5914-95 | 50µmoles | .053grams | .5 | 3.33 | 2 | 1.25 | .91 | .67 | .17 |
| Expedite | |||||||||
| Cat.No. | Pack Size | Grams/ Pack | Dilution (mL) | Molarity | 50nm | 0.2µm | 1µm | 15µm | |
| Approximate Number of Additions | |||||||||
| 10-5914-02 | 0.25grams | .25grams | 3.54 | .07 | 64.4 | 40.25 | 29.27 | 4.03 | |
| 10-5914-90 | 100µmoles | .105grams | 1.5 | .07 | 23.6 | 14.75 | 10.73 | 1.48 | |
| 10-5914-95 | 50µmoles | .053grams | .75 | .07 | 8.6 | 5.38 | 3.91 | .54 | |
| Beckman | |||||||||
| Cat.No. | Pack Size | Grams/ Pack | Dilution (mL) | Molarity | 30nm | 200nm | 1000nm | ||
| Approximate Number of Additions | |||||||||
| 10-5914-02 | 0.25grams | .25grams | 3.54 | .07 | 66 | 41.25 | 30 | ||
| 10-5914-90 | 100µmoles | .105grams | 1.5 | .07 | 25.2 | 15.75 | 11.45 | ||
| 10-5914-95 | 50µmoles | .053grams | .75 | .07 | 10.2 | 6.38 | 4.64 | ||
08/15/2012 | http://www.glenres.com/ProductFiles/10-5914.html