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Oligo Synthesis

Oligo Synthesis : Click Chemistry

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5-Ethynyl-dU-CE Phosphoramidite

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

Glen Research

Catalogue No.DescriptionPack SizePriceQty
10-1554-025-Ethynyl-dU-CE Phosphoramidite0.25 g £850.00 Quantity Add to Order
10-1554-905-Ethynyl-dU-CE Phosphoramidite100 umole £259.00 Quantity Add to Order
10-1554-955-Ethynyl-dU-CE Phosphoramidite50 umole £141.00 Quantity Add to Order

Description

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.
 
 
Formula: C41H47N4O8P 
M.W.: 754.81 
F.W.: 314.19 

Diluent: Anhydrous Acetonitrile

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.

Storage: Freezer storage, -10 to -30°C, dry

Stability in Solution: 1-2 days

Please Note: All products of baseclick are patent protected and available in collaboration with baseclick.  Baseclick GmbH has filed the following patent applications: 1. WO2006/117161, New labelling strategies for the sensitive detection of analytes. 2. WO2008/952775, Click Chemistry for the production of reporter molecules. Baseclick GmbH holds a worldwide license for the research market of the "Click Chemistry" patent from "The Scripps Research Institute": 3. WO03/101972, Copper-catalysed ligation of azides and acetylenes.

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Protocols

MSDS

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References

Glen Report 25.24: New Products - TEMPO Spin Labels for Click Chemistry and 5-Ethynyl-dU

Glen Report 26.27: Technical Brief – Use of Click Chemistry for Possible Crosslinking, Click Synthesis of a Potentially Useful azido support

Glen Report 28.2: New Product - TIPS-5-Ethynyl-dU-CE Phosphoramidite

  • 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.
  • C. J. Burrows, J. G. Muller, Chem. Rev. 1998, 98, 1109 – 1151.
  • T. R. Chan, R. Hilgraf, K. B. Sharpless, V. V. Fokin, Org. Lett. 2004, 6, 2853 – 2855.
  • 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.
  • P. M. E. Gramlich, S. Warncke, J. Gierlich, T. Carell, Angew. Chem. 2008, 120, 3491–3493; Angew. Chem. Int. Ed. 2008, 47, 3442– 3444.
  • P. M. E. Gramlich, C. T. Wirges, A. Manetto, T. Carell, Angew. Chem. Int. Ed. 2008, 47, 8350-8358.

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Applications & Benefits

DILUTION/COUPLING DATA

The table below shows pack size data and, for solutions, dilutions and approximate couplings based on normal priming procedures. Please link for more detailed usage information with the various synthesizers.

ABI 392/394
Cat.No. Pack Size Grams/ Pack 0.1M Dil. (mL) LV40 LV200 40nm 0.2µm 1µm 10µm
Approximate Number of Additions
10-1554-95 50µmoles .038grams .5 3.33 2 1.25 .91 .67 .17
10-1554-90 100µmoles .075grams 1 20 12 7.5 5.45 4 1
10-1554-02 0.25grams .25grams 3.31 97 58.2 36.38 26.45 19.4 4.85
Expedite
Cat.No. Pack Size Grams/ Pack Dilution (mL) Molarity 50nm 0.2µm 1µm 15µm  
Approximate Number of Additions
10-1554-95 50µmoles .038grams .75 .07 8.6 5.38 3.91 .54  
10-1554-90 100µmoles .075grams 1.5 .07 23.6 14.75 10.73 1.48  
10-1554-02 0.25grams .25grams 4.94 .07 92.4 57.75 42 5.78  
Mermade
Cat.No. Pack Size Grams/ Pack Dilution (mL) Molarity 30nm 200nm 1000nm    
Approximate Number of Additions
10-1554-95 50µmoles .038grams .75 .07 10.2 6.38 4.64    
10-1554-90 100µmoles .075grams 1.5 .07 25.2 15.75 11.45    
10-1554-02 0.25grams .25grams 4.94 .07 94 58.75 42.73

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