AP-dC-CE Phosphoramidite

1-[5'-O-(4,4'-Dimethoxytrityl)-β-D-2'-deoxyribofuranosyl]-9-(2-trifluoroacetamidoethoxy)-1,3-diaza-2-oxophenoxazine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]phosphoramidite

Product Specifications

Formula:
C49H54F3N6O10P
M.W.:
974.97
F.W.:
438.33
To Retrieve a Catalog Number, Select a Pack Size and Format:

Description

Substitution of C-5 propynyl-dC (pdC) for dC and C-5 propynyl-dU (pdU) for dT are effective strategies to enhance base pairing. Using these base substitutions, duplex stability and melting temperatures are raised by the following amounts: C-5 propynyl-C 2.8° per substitution; C-5 propynyl-U 1.7° per substitution. AP-dC (G-clamp) substitutes for dC and is another very important modified nucleoside that enhances hybridization by 7-21° per substitution depending upon the sequence and location of the AP-dC. The ability of these modified bases to enhance binding while maintaining specificity has proven useful in antisense research and in the synthesis of high affinity probes. AP-dC is also a fluorescent nucleoside and should find uses in DNA structural research.

Details

Usage

  • Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
  • Deprotection: AMA (Ammonium hydroxide/40% Methylamine 1:1 v/v) for 10 minutes at 65°C is recommended. (To prevent modification of dC by Methylamine, use Ac-dC (10-1015-xx) during synthesis.)
Specifications
Diluent Anhydrous Acetonitrile
Storage Refrigerated storage, maximum of 2-8°C, dry
Stability 24 hours


Dilution/Coupling Data

The table below show pack size data and, for solutions, dilution and approximate coupling based on normal priming procedures.

ABI 392/394

Catalog # Pack Size Grams/Pack 0.1M Dil. (mL) Approximate Number of Additions
LV40 LV200 40nm 0.2μm 1μm 10μm
10-1097-02 0.25 g .25grams 2.56 72 43.2 27 19.64 14.4 3.6
10-1097-90 100 µmol .097grams 1 20 12 7.5 5.45 4 1
10-1097-95 50 µmol .049grams 0.5 3.33 2 1.25 0.91 0.67 0.17

Expedite

Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-1097-02 0.25 g .25grams 3.83 0.07 70.2 43.88 31.91 4.39
10-1097-90 100 µmol .097grams 1.5 0.07 23.6 14.75 10.73 1.48
10-1097-95 50 µmol .049grams 0.75 0.07 8.6 5.38 3.91 0.54