5-Ethynyl uridine (5-EU)

Product Information

Fast and antibody free RNA Labeling without a Denaturation Step

5-EU is a highly effective uridine analogue for imaging global nascent RNA transcription both in vitro and in vivo [1]. Once incorporated into RNA at nascent transcription sites within a cell, the RNA can be fluorescently labeled without denaturation using the copper-catalyzed azide–alkyne cycloaddition (CuAAC) reaction, recognized in the 2022 Nobel Prize in Chemistry [2, 3]. This method delivers high sensitivity, clean backgrounds, and is faster and gentler than BrU-based assays.

Why buy 5-EU from baseclick?

• Market‑leading pricing with bulk options, consistent ≥ 98% HPLC purity, and rapid, reliable supply for research and development.
• Available Sizes: 10 mg, 100 mg, and bulk quantities upon request (research use only; not for diagnostic procedures).

What makes 5-EU different from other options?

• Click chemistry-based detection: Rapid, efficient dye conjugation to the ethynyl handle for bright, uniform signals.
• No RNA denaturation required: Preserves cell morphology and antigenicity, ideal for multiplexing with immunostaining.
• High signal‑to‑noise ratio: Strong, uniform fluorescence signals for robust detection and imaging.
• Broad compatibility: Works seamlessly with mammalian cells, organoids, and tissue sections; supports in vitro and in vivo research workflows.

How does 5-ethynyl uridine (5-EU) work?

Cell‑permeable 5‑EU is converted intracellularly to the triphosphate and incorporated into newly synthesized RNA, replacing uridine. The ethynyl group then reacts with azide‑modified tags as e.g. fluorophores via CuAAC, generating bright, specific labeling of nascent RNA.

Can 5-EU be used to generate functionalized mRNAs?

5-EU is well-suited to generate internally functionalized RNAs using mild and efficient click chemistry. Its ethynyl group allows for conjugation with azide‑modified moieties like fluorescent dyes, biotins, linkers or other tags.

EU-modified mRNA can be synthesized easily by replacing uridine triphosphate (UTP) by 5-EUTP in an in vitro transcription (IVT) [4]. For this purpose, we recommend using the baseScribe T7 High Yield IVT Kits, which are designed for fast and robust mRNA synthesis with excellent yield.

LITERATURE

[1] Exploring RNA transcription and turnover in vivo by using click chemistry, C. Y. Jao et al., 2008, Proc. Natl. Acad. Sci. U. S. A., Vol. 105, p. 15779–15784.

https://doi.org/10.1073/pnas.0808480105

[2] Peptidotriazoles on Solid Phase: [1,2,3]-Triazoles by Regiospecific Copper(I)-Catalyzed 1,3-Dipolar Cycloadditions of Terminal Alkynes to Azides., W. Tornøe, C. Christensen, M. Meldal J. Org. Chem. 2002, 67, 3057-3064.

[3] A Stepwise Huisgen Cycloaddition Process: Copper(I)-Catalyzed Regioselective “Ligation” of Azides and Terminal Alkynes., V. Rostovtsev, L. G. Green, V. V. Fokin, K. B. Sharpless, Angew. Chemie Int. Ed. 2002, 41, 2596–2599.

[4] 5-Ethynyluridine: A Bio-orthogonal Uridine Variant for mRNA-Based Therapies and Vaccines. Maassen, B. Coenen, S.-L. Dülk, M. van der Werff, H. Warner, F. Spada, T. Frischmuth, D. Incarnato, G. van den Bogaart, ChemBioChem 2023, 24, e202200658.

Capturing the interactome of newly transcribed RNA, X. Bao et al., 2018, Nature Methods, Vol. 15, p. 213-220.

https://doi.org/10.1038/nmeth.4595

Visualization of the Nucleolus Using Ethynyl Uridine, M. Dvořáčková et al., 2018, Frontiers in Plant Science, Vol. 9(177).

https://doi.org/10.3389/fpls.2018.00177