5-Ethynyl-dU-CE Phosphoramidite

5'-Dimethoxytrityl-5-ethynyl-2'-deoxyUridine, 3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite

Product Specifications

CAS Number:
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5-Ethynyl-dU offers convenient click conjugation with an azide to generate a label rigidly attached to one of the oligonucleotide bases. 5-Ethynyl-dU is subject to base-catalyzed hydration during cleavage and deprotection, especially when using a strong base or heat. Hydration of an ethynyl group forms a methyl ketone which subsequently blocks potential click reactions. Mild deprotection conditions are necessary when using 5-Ethynyl-dU-CE Phosphoramidite to prevent this side reaction. TIPS-5-Ethynyl-dU-CE Phosphoramidite, containing a protected alkyne, offers broader compatibility with oligonucleotide synthesis and deprotection. Protecting the 5-ethynyl group with a triisopropylsilyl (TIPS) protecting group prevents acid or base catalyzed hydration during oligonucleotide synthesis and workup. A quick treatment with TBAF removes the TIPS protecting group.



  • Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
  • Deprotection: Use ammonium hydroxide and deprotect at room temperature as required by nucleobases. Compatible with UltraMild deprotection. Not compatible with methylamine deprotection.
Diluent Anhydrous Acetonitrile
Storage Freezer storage, -10 to -30C, dry
Stability 1-2 days

Intellectual Property

baseclick GmbH has been granted the following patents (1-3) besides its further patent applications (4-5). |1. WO  2006/117161  (New  labelling  strategies  for  the  sensitive detection of analytes)|2. WO 2008/952775 (Click chemistry for the production of reporter molecules)|3. WO 2010/115957 (Click Chemistry on heterogeneous catalysts)|4. PCT/EP 2013/064610 (Anandamide-modified nucleic molecules)|5. PCT/EP 2015/056007 (Self-assembly of DNA Origami: a diagnostic tool)|baseclick GmbH holds a worldwide exclusive license for granted patent application|WO 03/101972 (Copper-catalysed ligation of azides and acetylenes  for  the  nucleic  acid field) in the area of diagnostics and research. As Glen Research and baseclick are partners, Glen Research is now able to help in sublicensing this outstanding technology.

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
10-1554-02 0.25 g .25grams 3.31 97 58.2 36.38 26.45 19.4 4.85
10-1554-90 100 µmol .075grams 1 20 12 7.5 5.45 4 1
10-1554-95 50 µmol .038grams 0.5 3.33 2 1.25 0.91 0.67 0.17


Catalog # Pack Size Grams/Pack Dilution (mL) Approximate Number of Additions
Molarity 50nm 0.2μm 1μm 15μm
10-1554-02 0.25 g .25grams 4.94 0.07 92.4 57.75 42 5.78
10-1554-90 100 µmol .075grams 1.5 0.07 23.6 14.75 10.73 1.48
10-1554-95 50 µmol .038grams 0.75 0.07 8.6 5.38 3.91 0.54


REFERENCE(S)| 1 C.W. Tornoe, C. Christensen, M. Meldal, J. Org. Chem. 2002, 67, 3057-3064; V. V. Rostovtsev, L. G. Green, V. V. Fokin, K. B. Sharpless, Angew. Chem. 2002, 114, 2708-2711; Angew. Chem. Int. Ed. 2002, 41, 2596-2599.| 2 C. J. Burrows, J. G. Muller, Chem. Rev. 1998, 98, 1109 – 1151.| 3 T. R. Chan, R. Hilgraf, K. B. Sharpless, V. V. Fokin, Org. Lett. 2004, 6, 2853 – 2855.| 4 J. Gierlich, G. A. Burley, P. M. E. Gramlich, D. M. Hammond, T. Carell, Org. Lett. 2006, 8, 3639-3642. F. Seela, V. R. Sirivolu, Chem. Biodiversity 2006, 3, 509-514.| 5 P. M. E. Gramlich, S. Warncke, J. Gierlich, T. Carell, Angew. Chem. 2008, 120, 3491–3493; Angew. Chem. Int. Ed. 2008, 47, 3442– 3444.| 6 P. M. E. Gramlich, C. T. Wirges, A. Manetto, T. Carell, Angew. Chem. Int. Ed. 2008, 47, 8350-8358.