dP-CE Phosphoramidite

6H,8H-3,4-dihydro-pyrimido[4,5-c][1,2]oxazin-7-one,8-[(5'-dimethoxytrityl-ß-D-deoxyribofuranosyl),3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

Product Specifications

Formula:
C41H50N5O8P
M.W.:
771.85
F.W.:
330.23
To Retrieve a Catalog Number, Select a Pack Size and Format:

Description

The design of primers is frequently complicated by the degeneracy of the genetic code. Three strategies are now available to confront this problem. In the first, a mixed base addition (N) is used to form the degenerate site. This approach is best if the number of degenerate sites is small. A second option is the use of 2'-deoxyInosine or 2'-deoxyNebularine which exhibit low, but unequal, hydrogen bonding to the other four bases. The third option is the use of a universal nucleoside. In this strategy, the base analog does not hybridize significantly to the other four bases and makes up some of the duplex destabilization by acting as an intercalating agent. 3-Nitropyrrole 2'-deoxynucleoside (M) is the first example of a set of universal bases. Subsequently, 5-nitroindole was determined to be an effective universal base and to be superior to 3-nitropyrrole, based on duplex melting experiments. The modified bases designated P and K show considerable promise as degenerate bases. The pyrimidine derivative P, when introduced into oligonucleotides, base pairs with either A or G, while the purine derivative K base pairs with either C or T. A dP+dK mix also can serve as a mixed base with much less degeneracy than dA+dC+dG+dT (N).

Details

Usage

  • Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
  • Deprotection: No changes needed from standard method recommended by synthesizer manufacturer.
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
10-1047-02 0.25 g .25grams 3.24 94.67 56.8 35.5 25.82 18.93 4.73
10-1047-90 100 µmol .077grams 1 20 12 7.5 5.45 4 1

Expedite

Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-1047-02 0.25 g .25grams 4.83 0.07 90.2 56.38 41 5.64
10-1047-90 100 µmol .077grams 1.5 0.07 23.6 14.75 10.73 1.48