Alkyne Phosphoramidite, 5'-terminal | CAS 1417539-32-2

Alkyne Phosphoramidite, 5'-terminal is a nucleic-acid building block designed for incorporating an alkyne handle at the 5′ end of oligonucleotides during automated DNA/RNA synthesis. This reagent enables downstream click chemistry labeling workflows, allowing researchers to attach fluorophores, affinity tags, or biomolecular payloads to sequence-defined strands for fluorescence imaging, assay development, and molecular diagnostics research. The 5′-terminal alkyne placement supports conjugation strategies where accessibility at the strand terminus is important for probe performance.

1. Oligonucleotide Click Labeling

Alkyne Phosphoramidite, 5'-terminal is used to generate 5′-functional oligonucleotides bearing a terminal alkyne for CuAAC or related click conjugation workflows. Researchers commonly incorporate this handle into primers, probes, or guide strands and then perform post-synthetic conjugation with azide-bearing fluorophores, biotin/streptavidin tags, or other detection moieties. This approach is frequently applied in fluorescence-based nucleic acid assays where the labeling position at the 5′ terminus helps maintain hybridization behavior while enabling robust signal readout.

2. Fluorescent Nucleic Acid Probes

Alkyne Phosphoramidite, 5'-terminal supports the construction of fluorescence imaging and detection reagents by enabling site-specific attachment of fluorescent dyes to oligonucleotides. In molecular biology and chemical biology laboratories, sequence-defined probes are synthesized with the 5′ alkyne and subsequently conjugated to dye-azides to produce labeled hybridization probes for microscopy workflows and fluorescence plate assays. Terminal labeling is particularly useful when the experimental design benefits from a defined probe geometry and consistent fluorophore placement relative to the binding sequence.

3. Molecular Beacon and Probe Engineering

Alkyne Phosphoramidite, 5'-terminal is used in nucleic acid probe engineering where controlled end-group functionalization is required to build signal-responsive fluorescent constructs. Researchers often synthesize beacon-like or structured oligonucleotides with a 5′ alkyne handle and then click-conjugate reporting groups (e.g., dyes or quencher partners) to create fluorescence readouts tied to hybridization or conformational changes. This workflow is valuable for developing sequence-specific fluorescence reagents for real-time monitoring and nucleic acid analysis method development.

4. Surface Immobilized DNA Sensors

Alkyne Phosphoramidite, 5'-terminal is leveraged to prepare alkyne-functional oligonucleotides that can be immobilized or patterned on azide-presenting surfaces through click chemistry. Materials and biosensor development teams use 5′-alkyne strands to create DNA-modified interfaces for hybridization-based sensing platforms, including microarray-style formats and surface-tethered probe layers used in fluorescence readout workflows. Terminal alkyne placement helps ensure that the immobilized probe presents its recognition sequence effectively while positioning the attachment chemistry away from the hybridizing region.