Click chemistry-generated, internal dye-labeled oligonucleotides

Learn about "click chemistry" reactions, used to join small chemical subunits in a modular fashion, yielding singular reaction products that are typically physiologically stable and stereospecific.

Sep 12, 2011

Revised/updated Jul 7, 2016

In general terms, “click chemistry” describes reactions used to join small chemical subunits in a modular fashion, yielding singular reaction products that are typically physiologically stable and stereospecific. It is an option for complex oligonucleotide synthesis when traditional methods provide less than optimal results. Oligonucleotide chemistry applications make use of azide alkyne Huisgen cycloaddition, a two-step process that uses quantitative chemical reactions of alkyne and azide moieties to create covalent carbon-heteroatom bonds between biochemical species [1]. Copper(I) acts as a catalyst to form a 1,2,3-triazole between an azide and terminal alkyne [2]. These reactions are strongly exothermic and so exhibit a large thermodynamic driving force. The technology is reliable and stable, making it an ideal oligonucleotide labeling method.

Some of the benefits of this click chemistry reaction include:

  • Occurs in aqueous solution, at room temperature
  • Stable toward H2O, O2, and under most organic synthesis conditions
  • Does not have side reactions
  • Is a robust catalytic process
  • Lacks functional group interference
  • Yields a thermally and hydrolytically stable triazole connection
  • Offers an unprecedented level of selectivity, reliability, and scope for syntheses that require covalent linkages between biochemical species
Modification name Used for modifying oligos that have:
5′, Int, 3′ Azide (NHS Ester) 5′, 3′, or internal azide functional group
5′ Hexynyl 5′ alkyne functional group
5′, Int, 3’ 5-Octadiynyl dU 5′, 3′, or internal alkyne functional group
5′, Int Biotin (Azide) 5′ or internal biotin functional group
5′, Int 6-FAM (Azide) 5′ or internal 6-FAM functional group
5′, Int 5-TAMRA (Azide) 5′ or internal 5-TAMRA functional group

To order an alkyne- or azide-modified oligonucleotide: specify the nucleic acid sequence along with the appropriate alkyne or azide modifications included in the sequence.

To order an oligonucleotide modified by a 1,2,3-triazole linkage of biotin, 6-FAM, or 5-TAMRA: select the desired azide modification at the desired location within the nucleic acid sequence. IDT will synthesize the oligonucleotide, perform the click chemistry reaction, and purify the product.

References

  1. Rostovtsev VV, Green LG, et al. (2002) A stepwise Huisgen cycloaddition process: copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angew Chem Int Ed Engl, 41(14): 2596−2599. 
  2. Moses JE and Moorhouse AD. (2007) The growing applications of click chemistry. Chem Soc Rev, 36(8): 1249−1262.

Click chemistry-enabled, modified oligonucleotides are manufactured and sold under license from baseclick GmbH, using baseclick’s proprietary click chemistry. All such modified products are sold by IDT for the end-user’s internal research purposes only. See www.baseclick.org for further details.

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