DBCO-dT-CE Phosphoramidite

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10-1539

5'-Dimethoxytrityl-5-[(6-oxo-6-(dibenzo[b,f]azacyclooct-4-yn-1-yl)-capramido-N-hex-6-yl)-3-acrylimido]-2'-deoxyUridine,3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

Formula:
C69H80N7O11P
M.W.:
1214.57
F.W.:
773.77
Catalog: Make Selections to Reveal

Description

At Glen Research, our goal was to offer a copper-free click phosphoramidite reagent with the following properties:

  • Simple to use
  • Stable in solution on the synthesizer
  • Stable to ammonium hydroxide and AMA
  • Excellent click performance in 17 hours or less at room temperature

From the variety of cyclooctyne-based copper-free click reagents so far described, we have chosen to offer compounds based on a dibenzo-cyclooctyne (DBCO) structure. We are offering 5'-DBCO-TEG Phosphoramidite for preparing oligos with a 5'-DBCO modification and DBCO-dT-CE Phosphoramidite for inserting a DBCO group at any position within the oligonucleotide. DBCO-sulfo-NHS Ester is also offered for post-synthesis conjugation reactions. DBCO-modified oligos may be conjugated with azides in organic solvents, such as DMSO, or aqeous buffers. Depending on the azide used, the reaction will go to completion in 4-17 hours at room temperature. Simple desalting on a Glen Gel-Pak™ leads to a product with virtually quantitative conjugation efficiency.

Note: We now recommend that synthesis of oligos containing DBCO-dT be completed using 0.5 M CSO in anhydrous acetonitrile (40-4632-xx). Acceptable results can be achieved with iodine oxidation if DBCO-dT is subjected to no more than 8-10 cycles.

Details

Usage

  • Coupling: 12 minute coupling time recommended. Note the DBCO-dT is susceptible to damage by iodine during oxidation. To prevent loss of the DBCO label, use 0.5M CSO in anhydrous acetonitrile (40-4632-xx) and a 3 minute oxidation time for best results.
  • Deprotection: As required by nucleobases. Compatible with 30% ammonium hydroxide for 2 hours at 65°C or 17 hours at room temperature. AMA (ammonium hydroxide/40% methylamine 1:1) for 2 hours at room temperature will give acceptable results.
Specifications
Diluent Anhydrous Acetonitrile/Dichloromethane 1:3 (v/v)
Storage Freezer storage, -10 to -30°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
10-1539-02 0.25 g .25grams 2.06 55.33 33.2 20.75 15.09 11.07 2.77
10-1539-90 100 µmol .121grams 1 20 12 7.5 5.45 4 1
10-1539-95 50 µmol .061grams 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
10-1539-02 0.25 g .25grams 3.07 0.07 55 34.38 25 3.44
10-1539-90 100 µmol .121grams 1.5 0.07 23.6 14.75 10.73 1.48
10-1539-95 50 µmol .061grams 0.75 0.07 8.6 5.38 3.91 0.54