endo-BCN CE-phosphoramidite | CAS 1352811-59-6

Endo-BCN CE-phosphoramidite is a BCN (bicyclononyne) cyclooctyne–derived click chemistry building block provided in a CE-phosphoramidite form for efficient incorporation into nucleic acid architectures. As a strain-promoted cyclooctyne click reagent, it enables copper-free, bioorthogonal labeling of azide-bearing targets, which is highly valued in chemical biology workflows where compatibility with sensitive biomolecules is required. The phosphoramidite format supports automated solid-phase synthesis, making endo-BCN CE-phosphoramidite a practical choice for preparing azide-reactive oligonucleotide conjugates, imaging probes, and functional nucleic-acid materials.

1. Oligonucleotide Click Labeling

Endo-BCN CE-phosphoramidite is used to install a BCN click handle directly into DNA or RNA constructs during automated phosphoramidite synthesis, enabling downstream copper-free conjugation to azide-functional partners. Research groups commonly apply BCN-bearing oligonucleotides to generate sequence-defined probes, affinity reagents, and multivalent labeling tools where the click site needs to be positioned at specific internal or terminal locations. This approach is particularly useful for preparing oligonucleotide conjugates for microscopy, flow-based assays, and mechanistic studies that require modular attachment of dyes, linkers, or reporter moieties via azide chemistry.

2. Molecular Imaging Probe Conjugation

Endo-BCN CE-phosphoramidite supports the preparation of nucleic-acid–based imaging reagents that can be post-functionalized with azide-tagged fluorophores, quenchers, or other signal reporters. In molecular imaging and probe development pipelines, BCN-modified oligonucleotides provide a stable, bioorthogonal handle that can be coupled to imaging components under conditions compatible with delicate labeling chemistries. The CE-phosphoramidite delivery format helps streamline probe manufacturing by integrating the click functionality into the oligonucleotide synthesis step, reducing variability associated with late-stage functionalization.

3. Bioorthogonal Targeting Platforms

Endo-BCN CE-phosphoramidite is widely used in chemical biology to build targeting and recognition platforms that rely on nucleic-acid scaffolds carrying a defined click-reactive group. By incorporating BCN into probes, researchers can generate modular systems that couple to azide-bearing ligands, polymers, or nanoparticles without introducing copper catalysts that may interfere with biomolecular integrity. Such BCN-functional oligonucleotide platforms are frequently used to create multicomponent binding constructs, surface-tethered reagents, and library-style probe sets where consistent conjugation chemistry is essential.

4. Functional Nucleic-Acid Materials

Endo-BCN CE-phosphoramidite is applicable to the fabrication of functional nucleic-acid materials, including programmable assemblies and surface-anchored architectures that require precise placement of reactive handles. Materials scientists and biomaterials researchers use BCN-modified oligonucleotides as addressable connection points for azide-functional crosslinkers, surface coatings, or modular building blocks during material assembly. The phosphoramidite format enables scalable preparation of BCN-bearing strands, supporting reproducible construction of nucleic-acid-based networks, responsive materials, and template-directed conjugation schemes used in advanced materials development.