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Oligo Synthesis

Oligo Synthesis : CEPs

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Pac-dA-CE Phosphoramidite

Pac-dA-CE Phosphoramidite

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-1601-02Pac-dA-CE Phosphoramidite 0.25g £18.00 Quantity Add to Order
10-1601-05Pac-dA-CE Phosphoramidite 0.5g £36.00 Quantity Add to Order
10-1601-10Pac-dA-CE Phosphoramidite 1.0g £73.00 Quantity Add to Order

Description

Pac-dA-CE Phosphoramidite

Structure

Catalog Number: 10-1601-xx

Description: Pac-dA-CE Phosphoramidite

5'-Dimethoxytrityl-N-phenoxyacetyl-2'-deoxyAdenosine,
3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite
Formula: C48H54N7O8P M.W.: 887.97 F.W.: 313.21

Diluent: Anhydrous Acetonitrile
Coupling: No changes needed from standard method recommended by synthesizer manufacturer. 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).
Deprotection: UltraMILD deprotection: 0.05M Potassium Carbonate in Methanol, 4 hours at Room Temperature OR 2 hours at Room Temperature in 30% Ammonium Hydroxide Technical Bulletin
Storage: Freezer storage, -10 to -30°C, dry
Stability in Solution: 24 hours

ULTRAMILD CE PHOSPHORAMIDITES

The synthesis of labelled oligonucleotides has become a standard procedure in many laboratories and many labelling reagents, e.g., biotin and fluorescein, are now available as ß-cyanoethyl (CE) phosphoramidites. Labels which are currently available as CE phosphoramidites have one common property - they must be stable to the strongly alkaline conditions required for removal of the base protecting groups. This property is lacking in several interesting dyes and labels. We sought an alternative protecting scheme for the normal CE phosphoramidites which would allow UltraMILD deprotection and would not react with a wider variety of tags and labels. A set of monomers using phenoxyacetyl (Pac) protected dA and 4-isopropyl-phenoxyacetyl (iPr-Pac) protected dG, along with acetyl protected dC, met the desired criteria for UltraMILD deprotection.

We recommend the use of phenoxyacetic anhydride (Pac2O) in Cap A. This modification removes the possibility of exchange of the iPr-Pac protecting group on the dG with acetate from the acetic anhydride capping mix. Cleavage and deprotection can be carried out in 2 hours at room temperature with ammonium hydroxide or 4 hours with 0.05M potassium carbonate in methanol.

Isobutyryl (iBu) protected dA has been discontinued. Pac-dA is the replacement.

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Protocols

Material Safety Data Sheet

Glen Report 11.2: Alternatives To Expedite Monomers


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Applications & Benefits

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
10-1601-02 0.25grams .25grams 2.82 80.67 48.4 30.25 22 16.13 4.03
10-1601-05 0.5grams .5grams 5.63 174.33 104.6 65.38 47.55 34.87 8.72
10-1601-10 1.0gram 1grams 11.26 362 217.2 135.75 98.73 72.4 18.1
Expedite
Cat.No. Pack
Size
Grams/
Pack
Dilution
(mL)
Molarity 50nm 0.2µm 1µm 15µm
Approximate Number of Additions
10-1601-02 0.25grams .25grams 4.2 .07 77.6 48.5 35.27 4.85
10-1601-05 0.5grams .5grams 8.4 .07 161.6 101 73.45 10.1
10-1601-10 1.0gram 1grams 16.81 .07 329.8 206.13 149.91 20.61
Beckman
Cat.No. Pack
Size
Grams/
Pack
Dilution
(mL)
Molarity 30nm 200nm 1000nm

Approximate Number of Additions
10-1601-02 0.25grams .25grams 4.2 .07 79.2 49.5 36

10-1601-05 0.5grams .5grams 8.4 .07 163.2 102 74.18

10-1601-10 1.0gram 1grams 16.81 .07 331.4 207.13 150.64

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Related products

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