Perylene dU phosphoramidite | CAS 908117-78-2

Perylene dU phosphoramidite is a fluorescent, nucleoside-derived phosphoramidite designed for incorporation of a perylene dye into oligonucleotides via standard DNA/RNA synthesis workflows. As a click-chemistry-adjacent reagent, it supports downstream conjugation strategies where dye-labeled nucleic acids are subsequently functionalized for bioorthogonal coupling, imaging, or probe assembly. The perylene core provides strong photophysical properties and high signal stability, making it attractive for sensitive molecular detection and materials labeling where robust fluorescence is required.

1. Fluorescent Oligonucleotide Probes

Perylene dU phosphoramidite is widely used to generate DNA or RNA probes that require bright, photostable labeling for hybridization-based assays and nucleic acid tracking in complex experimental workflows. Researchers incorporate the dye-bearing nucleoside during solid-phase oligonucleotide synthesis to create sequence-defined fluorescent strands for studying binding, kinetics, and structural changes. The resulting labeled oligonucleotides are commonly used as imaging reagents in molecular biology toolkits, including fluorescence microscopy and plate-based readouts, where long-lived fluorescence improves signal-to-background under extended acquisition times.

2. Bioorthogonal Conjugation Handles

Perylene dU phosphoramidite is frequently selected in projects that combine fluorescent nucleic acid labeling with subsequent bioconjugation steps, including click-chemistry workflows that attach the oligonucleotide to targeting ligands, surfaces, or carrier scaffolds. By placing the perylene label at a defined position within the nucleic acid, the probe can serve as a fluorescent reporter while additional functional groups introduced elsewhere on the construct enable orthogonal coupling. This approach supports modular build strategies for creating multi-component imaging reagents, such as dye-labeled oligonucleotide conjugates used to map biomolecular interactions or to generate fluorescent tagging standards for assay development.

3. Molecular Imaging and FRET Assays

Perylene dU phosphoramidite is used to prepare fluorescent nucleic acid constructs for molecular imaging experiments and distance-dependent fluorescence measurements, including FRET-based assay formats. The perylene dye is valued for its strong emission and resistance to photobleaching, which helps maintain signal quality during repeated imaging cycles or time-resolved measurements. In fluorescence-based studies, labeled oligonucleotides can be paired with complementary dye partners or quencher-bearing strands to create robust reporter systems for monitoring hybridization events, conformational dynamics, and nucleic-acid-dependent assembly processes.

4. Nucleic Acid–Based Biomaterials

Perylene dU phosphoramidite is also applied in biomaterials science to create fluorescent, sequence-defined nucleic acid components for constructing responsive materials and labeled scaffolds. Incorporating the dye-bearing nucleoside into functional oligonucleotides enables visualization of nucleic-acid-driven assembly, such as strand displacement networks, DNA nanostructure formation, and surface-tethered hybridization layers. These fluorescent oligonucleotide building blocks are commonly used to characterize material organization, stability, and spatial patterning in research settings, where durable fluorescence supports microscopy and quantitative imaging of nucleic-acid architectures.