C8-Alkyne-dU-CE Phosphoramidite

Site-specific alkyne-modified nucleoside for oligonucleotide labeling via click chemistry

C8-Alkyne-dU-CE Phosphoramidite is a chemically modified nucleoside designed for efficient, site-specific incorporation into DNA, RNA, or PNA strands during solid-phase oligonucleotide synthesis. Featuring a C8 alkyne spacer at the C5 position of deoxyuridine, this phosphoramidite enables robust bioorthogonal labeling via copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC).

The long, flexible octadiynyl chain significantly improves accessibility for post-synthetic modifications, making this building block ideal for developing functionalized probes, bioconjugates, and labeled oligonucleotides.

Chemical features

Backbone: Deoxyuridine (dU) base

C8 Spacer: Octadiynyl chain for improved flexibility and labeling access

5′-Hydroxyl Protection: DMT group for controlled synthesis

Phosphoramidite Group: 2-cyanoethyl (CE) for high coupling efficiency

This structural configuration supports efficient, stable, and high-yield incorporation into oligonucleotides under standard solid-phase synthesis conditions.

C8-Alkyne-dU-CE Phosphoramidite is a modified nucleoside designed for oligonucleotide synthesis, featuring a C8 spacer that enhances flexibility and accessibility for click chemistry reactions.

Earlier alkynyl-modified phosphoramidites had short, rigid linkers that limited conjugation efficiency and often interfered with duplex stability and hybridization performance.

C8-Alkyne-dU-CE offers:

• Improved click accessibility due to a longer flexible linker
• High retention of hybridization capacity — no disruption of DNA duplex formation
• Slight duplex stabilization, making it suitable for TaqMan and other hybridization-dependent applications

Applications

• Site-specific labeling of oligonucleotides with azide-bearing molecules (fluorophores, peptides, biotin, etc.)
• Development of multiplexed imaging probes
• Construction of click-functionalized TaqMan qPCR probes
• Dual or triple labeling for diagnostics and biosensing
• Functionalization for drug delivery or targeted therapeutics
• Real-time PCR, hybridization assays, FISH, and molecular barcoding

Technical Insight

Published research has demonstrated that oligonucleotides incorporating C8-Alkyne-dU maintain normal duplex stability and can even exhibit slight enhancement of melting temperatures, ensuring compatibility with hybridization-based techniques.

LITERATURE

Nucleosides And Oligonucleotides With Diynyl Side Chains: The Huisgen-Sharpless Cycloaddition “Click Reaction” Performed On Dna And Their Constituents, F. Seela et al., 2007, Nucleosides, Nucleotides & Nucleic Acids, Vol. 26, p. 597–601.

https://doi.org/10.1080/15257770701490308

DNA-Photographie: eine ultraempfindliche Methode zur Detektion von DNA mithilfe photographischer Techniken, D. M. Hammond et al., 2007, Angew. Chem., Vol. 119, p. 4262–4265.

https://doi.org/10.1002/ange.200605023

Transfer Printing of DNA by “Click” Chemistry, D. I. Rozkiewicz et al., 2007, ChemBioChem, Vol. 8, p. 1997–2002.

https://doi.org/10.1002/cbic.200700402

DNA Containing Side Chains with Terminal Triple Bonds: Base-Pair Stability and Functionalization of Alkynylated Pyrimidines and 7-Deazapurines, F. Seela et al., 2006, Chemistry & Biodiversity, Vol. 3, p. 509–514.

https://doi.org/10.1002/cbdv.200690054

Click Chemistry as a Reliable Method for the High-Density Postsynthetic Functionalization of Alkyne-Modified DNA, J. Gierlich et al., 2006, Org. Lett., Vol. 8, p. 3639–3642.

https://doi.org/10.1021/ol0610946

A click chemistry approach to developing molecularly targeted DNA scissors, T. Lauria et al., 2020, Chemistry – A European Journal, Vol. 26(70), p. 16782-16792.

https://doi.org/10.1002/chem.202002860

Supersensitive Multifluorophore RNA‐FISH for Early Virus Detection and Flow‐FISH by Using Click Chemistry, N. Raddaoui et al., 2020, ChemBioChem, Vol. 21(15), p. 2214-2218.

https://doi.org/10.1002/cbic.202000081

Selective targeting and degradation of doxorubicin-loaded folate-functionalized DNA nanocages, S. Raniolo et al., 2018, Nanomedicine: Nanotechnology, Biology and Medicine, Vol. 14(4), p. 1181-1190.

https://doi.org/10.1016/j.nano.2018.02.002