5-(Azidomethyl)-2'-deoxyuridine | CAS 59090-48-1

5-(Azidomethyl)-2'-deoxyuridine is a nucleoside analog bearing an azide handle, designed for bioorthogonal labeling and downstream click chemistry workflows. As a functionalized deoxyuridine derivative, it combines the compatibility of nucleoside scaffolds with the modular reactivity of azides, enabling efficient conjugation to complementary alkyne partners under copper(I)-catalyzed or strain-promoted click conditions. This reagent is widely used in chemical biology and biomaterials research where controlled incorporation of a clickable nucleoside motif supports imaging, tracking, and functionalization of nucleic-acid–related constructs.

1. Nucleoside Metabolic Labeling

5-(Azidomethyl)-2'-deoxyuridine is used as a clickable thymidine/deoxyuridine analog for metabolic incorporation into newly synthesized DNA in cultured cells and cell-free nucleic-acid systems. Researchers employ it to introduce an azide functionality at nucleic-acid positions, creating a substrate for subsequent conjugation with fluorescent alkynes, affinity tags, or other probe modules via click chemistry. This approach supports scalable labeling strategies for studying DNA dynamics, replication-associated processes, and nucleic-acid remodeling in experimental workflows that require post-incorporation derivatization. The azide-bearing methyl substituent provides a convenient handle for modular probe attachment without requiring direct chemical modification of every target biomolecule.

2. DNA Click-Functionalization Probes

5-(Azidomethyl)-2'-deoxyuridine is applied to generate DNA-derived probes and labeled nucleic-acid standards by coupling the incorporated azide groups to alkyne-bearing reporters. Common use cases include preparing fluorescent DNA constructs for microscopy and flow-based readouts, generating biotin or dye conjugates for pull-down and enrichment workflows, and producing labeled oligonucleotide fragments for analytical assays. Because the reagent installs clickable functionality within the nucleic-acid framework, it enables site-specific tagging at the level of DNA synthesis rather than after extensive end-labeling. This makes it particularly attractive for researchers building probe libraries where consistent labeling chemistry and flexible downstream conjugation are required.

3. Molecular Imaging of DNA Processes

5-(Azidomethyl)-2'-deoxyuridine supports molecular imaging workflows that rely on bioorthogonal click attachment of imaging agents to DNA. In practice, investigators incorporate the azide nucleoside into nucleic acids and then conjugate it to fluorophores or other imaging-compatible alkyne partners to visualize spatial and temporal patterns of DNA-associated events. The reagent’s nucleoside nature helps maintain compatibility with nucleic-acid labeling paradigms, while the azide handle offers a robust and modular route to install imaging functionality after incorporation. Such strategies are frequently used in chemical biology to map DNA localization, track nucleic-acid turnover, and compare labeling conditions across experimental sets using standardized click conjugation steps.

4. DNA-Templated Biomaterials

5-(Azidomethyl)-2'-deoxyuridine is used in biomaterials science to create clickable DNA scaffolds that can be further functionalized for material assembly and surface patterning. Researchers incorporate the azide nucleoside into DNA strands used as templates or structural components, then use click chemistry to attach polymers, crosslinkers, nanoparticles, or bioactive moieties bearing complementary alkyne functionality. This enables modular fabrication of DNA-based hydrogels, patterned coatings, and hybrid materials where the density and distribution of clickable sites can be tuned through nucleoside incorporation. The resulting materials benefit from the orthogonality of azide–alkyne conjugation, allowing functionalization under conditions compatible with sensitive biomolecular components.

5. Diagnostic Reagent Development

5-(Azidomethyl)-2'-deoxyuridine is employed to prepare labeled nucleic-acid reagents used as components in diagnostic-oriented assay development and analytical workflows. Developers use it to introduce azide groups into DNA or DNA-derived constructs, enabling post-synthesis attachment of detection chemistries such as fluorophores, enzyme tags, or affinity ligands through click conjugation. This strategy supports the creation of standardized probe formats for assay optimization, signal amplification schemes, and multiplexing designs where orthogonal labeling handles are advantageous. By separating nucleic-acid synthesis/incorporation from final reporter installation, the reagent streamlines reagent generation for research-grade assay development pipelines that require flexible and reproducible labeling chemistry.