Alkyne Amidite, hydroxyprolinol | CAS 1357289-02-1

Alkyne Amidite, hydroxyprolinol is an alkyne-functional phosphoramidite building block designed for incorporation of a terminal alkynyl handle into nucleic acids during automated solid-phase synthesis. The hydroxyprolinol-derived motif provides a stereodefined, hydroxyl-bearing scaffold that supports downstream conjugation workflows where click chemistry is used to attach fluorophores, affinity tags, or other reporter groups to modified oligonucleotides. In practice, this reagent is used by chemical biology and nucleic acid assay developers to generate clickable DNA or RNA probes for labeling, immobilization, and imaging reagent construction.

1. Oligonucleotide Click Labeling

Alkyne Amidite, hydroxyprolinol is used to introduce a terminal alkyne into DNA or RNA strands so that the resulting nucleic acid can be post-functionalized via copper-catalyzed azide-alkyne cycloaddition with azide-bearing reporters. Researchers commonly employ the alkyne-modified oligonucleotides to create fluorescently labeled probes for hybridization-based studies, to attach biotin or other affinity handles for pull-down workflows, and to build modular detection reagents where the same nucleic acid scaffold is decorated with different dyes or tags. This approach is particularly valuable in nucleic acid analysis workflows because the clickable handle is installed at a defined position during synthesis, enabling controlled placement of the labeling group for downstream assay readouts.

2. FISH And Imaging Probe Construction

Alkyne Amidite, hydroxyprolinol supports the development of fluorescence in situ hybridization (FISH) and related microscopy imaging probes by enabling site-specific attachment of fluorophores to oligonucleotide sequences. In microscopy and molecular imaging workflows, the alkyne handle provides a convenient conjugation point for attaching dye-azides or dye-containing linkers after oligonucleotide synthesis, allowing imaging reagent teams to tune labeling density and dye identity without changing the underlying probe sequence. This strategy is also used when constructing multicolor imaging panels, where different oligonucleotide probes are independently functionalized with distinct fluorescent reporters through the same click-compatible alkyne chemistry.

3. Surface Immobilized DNA Probes

Alkyne Amidite, hydroxyprolinol is frequently incorporated into oligonucleotides intended for immobilization on functional surfaces, including sensor chips, microarray slides, and assay platforms that require stable probe attachment. After synthesis, the terminal alkyne enables coupling to azide-functional linkers that can be tethered to surfaces or capture chemistries, supporting workflows where nucleic acid probes must be presented at defined densities for hybridization assays. Materials and biosensor developers use this reagent to create reusable probe layers for nucleic acid detection formats, where the click step provides a modular route from sequence synthesis to surface-ready probe conjugates.

4. Modular Affinity Reagent Building

Alkyne Amidite, hydroxyprolinol is used to generate clickable oligonucleotide conjugates for affinity-based research tools, including pull-down reagents and capture probes used in chemical biology. By installing an alkyne handle into the nucleic acid, teams can attach azide-functional affinity tags, such as biotin analogs or other capture moieties, to create sequence-specific reagents for enrichment and downstream characterization. This modular labeling approach helps assay development groups iterate on conjugate design—swapping reporter or capture components while keeping the nucleic acid recognition element constant—thereby streamlining reagent optimization for nucleic acid-driven workflows.