| Cyanine 3.5 Phosphoramidite |
Catalog Number: 10-5914-xx
Description: Cyananie 3.5 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 |
|
CYANINE LABELLING
Two cyanine derivatives, Cyanine 3 and Cyanine5 , which differ in structure simply by the number of carbons in the conjugated poly-ene linkage, are joined by the closely related analogues, Cyanine 3.5 and Cyanine 5.5, and are available as phosphoramidites. Cyanine dyes are normally added once at the 5’-terminus and the MMT group 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 more correctly. Cyanine dyes have also been used successfully adjacent to the 3’-terminus as long as 0.02M iodine oxidizer is used during the remainder of the synthesis.
Deprotection of oligos containing Cyanine dyes may be carried out with ammonium hydroxide at room temperature, regardless of the base protecting groups on the monomers used. If there is a need to use ammonium hydroxide at elevated temperature, Cyanine 3 and Cyanine 3.5 are more stable than Cyanine 5 and Cyanine 5.5. However, it is always prudent to use monomers with base labile protecting groups to limit the exposure time to 2 hours or less at 55°C.
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