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Oligo Synthesis

Oligo Synthesis : CEPs

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Cyanine 3.5 Phosphoramidite

Cyanine 3.5 Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-5914-02Cyanine 3.5 Phosphoramidite 0.25g £740.00£703.00Offer until : 31-Aug-2020Offer Code : GLEN55% off all Glen products View Offer Quantity Add to Order
10-5914-90Cyanine 3.5 Phosphoramidite 100µmoles £320.00£304.00Offer until : 31-Aug-2020Offer Code : GLEN55% off all Glen products View Offer Quantity Add to Order
10-5914-95Cyanine 3.5 Phosphoramidite 50µmoles £176.00£167.20Offer until : 31-Aug-2020Offer Code : GLEN55% off all Glen products View Offer Quantity Add to Order

Cyanine 3.5 Phosphoramidite

Cyanine 3.5 Phosphoramidite

Glen Research

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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Cyanine 3.5 Phosphoramidite

Cyanine 3.5 Phosphoramidite

Glen Research

Material Safety Data Sheet

Glen Report 21.2: Deprotection - Volume 3 - Dye-Containing Oligonucleotides

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Cyanine 3.5 Phosphoramidite

Cyanine 3.5 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. 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

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