Pac-2-Amino-dA-CE Phosphoramidite

5'-Dimethoxytrityl-N2-phenoxyacetyl-N6-di-n-butylaminomethylidene-2,6-diamino-2'-deoxypurine riboside-3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

Product Specifications

Formula:
C57H72N9O8P
M.W.:
1042.21
F.W.:
328.22
To Retrieve a Catalog Number, Select a Pack Size and Format:

Description

The simplest approach to the design of high affinity primers and probes is to substitute A sites with 2-amino-A, since the 2-amino-A-T base pair is equivalent in strength to the G-T base pair. 2-Amino-A also destabilizes A-G wobble mismatches, thus increasing specificity. In 1998, we introduced a 2-amino-dA monomer which exhibits fast and effective deprotection in ammonium hydroxide and it is stabilized to depurination during synthesis. We now recommend the use of 0.5 M CSO in anhydrous acetonitrile (40-4632-xx) for best results with multiple additions of 2-amino-dA. This is because the bis formamidine protected 2-amino-dA leads to significant strand scission when standard iodine oxidation is used during synthesis. For this reason, we have also added Pac-2-Amino-dA, a monomer with optimized protection to meet the following criteria: stable during oligonucleotide synthesis, oxidation, and detritylation; labile towards common deprotection conditions (NH3, AMA, MeNH2); and the nucleobase protecting groups are cleaved under fairly mild conditions.

Details

Usage

  • Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
  • Deprotection: 30% Ammonium Hydroxide for 4 hours at 65 °C or 8-17 hours at 55 °C. Compatible with 30% Ammonium Hydroxide/40% Methylamine 1:1 (AMA) for 20 minutes at 65 °C.
Specifications
Diluent Anhydrous Acetonitrile
Storage Refrigerated storage, maximum of 2-8°C, dry
Stability 1-2 days


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
10-1585-02 0.25 g .25grams 2.4 66.67 40 25 18.18 13.33 3.33
10-1585-90 100 µmol .104grams 1 20 12 7.5 5.45 4 1
10-1585-95 50 µmol .052grams 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
10-1585-02 0.25 g .25grams 3.58 0.07 65.2 40.75 29.64 4.08
10-1585-90 100 µmol .104grams 1.5 0.07 23.6 14.75 10.73 1.48
10-1585-95 50 µmol .052grams 0.75 0.07 8.6 5.38 3.91 0.54