dA-PACE Phosphoramidite

5'-Dimethoxytrityl-N-benzoyl-2'-deoxyAdenosine, 3'-O-(N,N-diisopropylamino)-phosphinyl-1,1-dimethyl-2-cyanoethyl acetate

Product Specifications

Formula:
C51H58N7O8P
M.W.:
928.02
F.W.:
354.24
To Retrieve a Catalog Number, Select a Pack Size and Format:

Description

Phosphonoacetate (PACE) modified oligonucleotides show great potential as biological modifiers in a wide variety of research applications. PACE monomers are part of a family of Phosphonocarboxylate monomers. The monomers can be easily incorporated into complex oligonucleotides and are compatible with a wide variety of other sugar or heterobase modifications. PACE DNA can be conjugated through the carboxylic acid functional group. They have been shown to be active in siRNA duplexes and accelerate the initial rate of cleavage by RNase H-1 when incorporated with phosphorothioates. However, the most interesting observation to date is that they exhibit an unprecedented enhancement in penetration of cultured cells. T

he phosphonoacetates are fully soluble in acetonitrile at a recommended concentration of 0.1M and are compatible with standard DNA synthesizers. A recommended coupling time of 33.3 minutes with 1H-Tetrazole is necessary when using the standard protocol. A modified LV cycle for AB instruments that reduces coupling time to 15 minutes with 1H-Tetrazole is available on our website. Oxidation must precede capping in the synthesis cycle. Reagents for oxidation depend on the type of synthesis. For fully modified oligos, we recommend the non-aqueous oxidizer camphorsulfonyloxaziridine (CSO) as a 0.1M solution. For mixed phosphodiester and phosphonoacetate modified oligos, a 0.5M CSO solution is recommended. Low water oxidizer, 40-4032, is an alternative oxidizing reagent although it has been reported that this can result in conversion of a small percentage of the phosphonoacetate to the phosphodiester. We also recommend the use of the Cap Mix B with DMAP (40-4020) instead of the standard Cap Mix B containing 1-Methylimidazole.

The standard protocol for cleavage and deprotection requires a two step method with pretreatment using 1,8-Diazabicyclo[5.4.0]undec-7-ene (DBU) and subsequent cleavage using methylamine. The DBU is used to deprotect the dimethylcyanoethyl (DMCE) protecting groups and to prevent alkylation of the bases during deprotection. Cleavage with 40% methylamine in water is recommended and we have also had good results when using AMA deprotection.

Details

Usage

  • Coupling: 33 minutes with 1H-Tetrazole Activator.||Synthesis: Oxidize before capping. Use either low water, low iodine oxidizer (Cat.# 40-4032-xx) or 10-camphorsulfonyloxaziridine (CSO) in acetonitrile. When CSO is used, extend the oxidation time to 3 minutes. Use 0.5M CSO when oxidizing mixed PACE/phosphodiester linkages. When oxidizing only PACE linkages, 0.1 M CSO can be used. For Cap Mix B, use 6.5% DMAP in THF (Cat.# 40-4020-xx). An example of a PACE cycle for AB synthesizers can be seen at:|http://www.glenresearch.com/Technical/PACE_cycle.pdf
  • Deprotection: Pretreat synthesis column with 1.5% DBU in anhydrous acetonitrile for 60 minutes (syringe method). Wash with acetonitrile and dry with argon. Deprotect with 40% Methylamine for 20 minutes at 55°C.
Specifications
Diluent Anhydrous Acetonitrile
Storage Freezer storage, -10 to -30°C, dry
Stability 2-3 days

Intellectual Property

These products are covered by patents, US 6,693,187 and 7,067,641, and patents pending owned by Metasense Technologies. Purchase of all or any of these products includes a limited license to use the products solely for the manufacture of oligonucleotides for research use only. This license specifically excludes the use of the product or oligonucleotides containing the product for: (a) therapeutic or diagnostic applications (including kits, pools, libraries and other products or services that incorporate oligonucleotides containing the product), (b) any in vivo toxicity/safety study in support of an investigational new drug application (or foreign counterpart), or (c) resale (including sale of kits, pools, libraries and other products or services that incorporate the product or oligonucleotides containing the product). If such activities have commercial application, a separate license is required from Metasense Technologies. Neither the product nor any product created through its use may be used in human clinical trials. A simple agreement must be signed before end-users and custom oligo services may purchase these products for use as defined above.


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
10-1140-02 0.25 g .25grams 2.69 76.33 45.8 28.63 20.82 15.27 3.82
10-1140-05 0.5 g .5grams 5.39 166.33 99.8 62.38 45.36 33.27 8.32
10-1140-10 1.0 g 1grams 10.78 346 207.6 129.75 94.36 69.2 17.3

Expedite

Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-1140-02 0.25 g .25grams 4.02 0.07 74 46.25 33.64 4.63
10-1140-05 0.5 g .5grams 8.04 0.07 154.4 96.5 70.18 9.65
10-1140-10 1.0 g 1grams 16.08 0.07 315.2 197 143.27 19.7