5-Ethynyl-dU-CE Phosphoramidite

Product Information

Click-ready nucleotide analog for site-specific DNA labeling and functionalization

5-Ethynyl-dU-CE Phosphoramidite is a synthetic nucleotide analog derived from 5-ethynyl-2′-deoxyuridine (EdU), featuring an ethynyl (–C≡CH) group at the 5-position of the nucleobase uracil. This alkyne moiety enables bioorthogonal labeling via copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), the foundation of click chemistry.

As a universal alkyne modifier, it integrates seamlessly into solid-phase DNA synthesis, offering high coupling efficiency and enabling site-specific functionalization for diverse applications from aptamer engineering to single-molecule sensing.

Before the introduction of 5-Ethynyl-dU-CE Phosphoramidite, DNA modification techniques were hampered by poor specificity, incompatibility with automated synthesis and biologically harsh reaction conditions.

This phosphoramidite solves these issues through smart design and clever chemistry:

• Click-ready alkyne: Enables selective conjugation with azides for labeling and bioconjugation.
• Solid-phase synthesis compatibility: Seamlessly fits into automated DNA synthesis workflows.
• Bioorthogonality: Chemically inert in biological systems until activated, allowing safe in vivo/in vitro use.
• Preserved DNA structure: The 5-position modification maintains Watson-Crick base pairing and duplex integrity

Applications

The versatility of 5-ethynyl-dU-CE-phosphoramidite extends over several areas:

1. Fluorescent imaging and FRET: Enables high-resolution DNA visualization.
2. Bioconjugation: Attaches DNA to proteins, nanoparticles, or surfaces.
3. Diagnostics & therapeutics: Powers biosensors, hybridization probes, and modified oligonucleotide drugs.
4. Cell proliferation assays: Related compounds like EdU revolutionized live-cell DNA synthesis tracking.
5. Click-SELEX and aptamer engineering: Essential for generating clickmers aptamers with enhanced binding and chemical diversity.
6. Programmable Nano-Reactors for Stochastic Sensing (PNRSS): In this cutting-edge platform, 5-Ethynyl-dU-CE enabled the creation of custom DNA strands with precisely placed alkyne handles.

5-Ethynyl-dU-CE Phosphoramidite is a cornerstone reagent in nucleic acid chemistry. By combining click chemistry compatibility, solid-phase synthesis efficiency, and protective strategies against hydration, it enables high-fidelity, modular DNA functionalization. Its role in aptamer development, molecular diagnostics, charge transport studies, and programmable nano-reactors [1] continue to drive innovation in synthetic biology, nanotechnology, and chemical biology.

[1] Programmable nano-reactors for stochastic sensing, S. Huang et al., Nat. Commun. 2021, 12, 5811.

Literature

DNA duplexes stabilized by modified monomer residues: synthesis and stability, D. Graham et al., 1998, J. Chem. Soc., Perkin Trans. 1, p. 1131–1138.

https://doi.org/10.1039/A707031D

A Versatile Modification of On-Column Oligodeoxynucleotides Using a Copper-Catalyzed Oxidative Acetylenic Coupling Reaction, N. Minakawa et al., 2003, J. Am. Chem. Soc., Vol. 125, p. 11545–11552.

https://doi.org/10.1021/ja036055t

Ethynyl Side Chain Hydration during Synthesis and Workup of “Clickable” Oligonucleotides: Bypassing Acetyl Group Formation by Triisopropylsilyl Protection, S. A. Ingale et al., 2013, J. Org. Chem., Vol. 78, p. 11271–11282.

https://doi.org/10.1021/jo401780u

Click Reaction on Solid Phase Enables High Fidelity Synthesis of Nucleobase-Modified DNA, F. Tolle et al., 2016, Bioconjugate Chem., Vol. 27, p. 500–503.

https://doi.org/10.1021/acs.bioconjchem.5b00668

Efficient Long-Range Hole Transport Through G-Quadruplexes, J. Wu et al., 2017, Chemistry – A European Journal, Vol. 23(56), p. 13980-13985.

https://doi.org/10.1002/chem.201702478

Pyrene-Modified DNA Aptamers with High Affinity to Wild-Type EGFR and EGFRvIII, E. Zavyalova et al., 2020, Nucleic Acid Therapeutics, Vol. 30(3), p. 175-187.

https://doi.org/10.1089/nat.2019.0830