N-methyl-N'-(azide-PEG3)-Cy3 | CAS 2107273-16-3

N-methyl-N'-(azide-PEG3)-Cy3 is a Cy3-based fluorescent labeling reagent bearing an azide-functionalized, PEG3 linker, designed for click chemistry bioconjugation workflows where a bright red/orange emission label is needed. The azide handle enables copper-catalyzed azide-alkyne cycloaddition (CuAAC) to attach Cy3 to biomolecules, peptides, and other targeting ligands under labeling conditions commonly used in chemical biology and fluorescence assay development.

1. Biomolecule Labeling

N-methyl-N'-(azide-PEG3)-Cy3 is used to introduce a Cy3 fluorophore onto proteins, peptides, and other biomolecular building blocks via azide-alkyne click conjugation. Researchers typically incorporate this reagent into labeling strategies where the PEG3 spacer helps reduce steric effects around the dye, supporting more consistent fluorescence readouts in downstream imaging, binding studies, and fluorescence-based assays. This reagent is especially useful when a modular labeling approach is preferred, allowing the Cy3 label to be installed onto alkyne-bearing biomolecules or affinity reagents to generate fluorescent conjugates for characterization and assay development.

2. Fluorescence Microscopy Tracing

N-methyl-N'-(azide-PEG3)-Cy3 supports fluorescence microscopy workflows that rely on covalent fluorescent tagging of biomolecular probes. In practice, investigators use it to build Cy3-labeled conjugates for cellular and extracellular labeling experiments, including tracking of labeled ligands, visualization of biomolecule distribution, and preparation of imaging reagents for confocal or widefield fluorescence microscopy. The PEG3 linker and azide functionality make it convenient for constructing microscopy-compatible conjugates from alkyne-functional partners, enabling reproducible fluorescent staining reagents for experimental workflows that require defined dye placement.

3. Flow Cytometry Conjugates

N-methyl-N'-(azide-PEG3)-Cy3 is frequently employed to prepare Cy3-labeled conjugates for flow cytometry and fluorescence-based cell analysis. By installing the Cy3 label through click chemistry onto alkyne-bearing antibodies, peptides, or other binding reagents, researchers generate fluorescent reagents that can be used to monitor binding, uptake, or surface association in assay formats compatible with standard flow cytometers. The azide-PEG3 design supports flexible conjugate construction, allowing the dye to be appended to targeting ligands in a controlled manner for multiplexing workflows where Cy3 emission is part of the chosen detection panel.

4. Click-Designed Probe Construction

N-methyl-N'-(azide-PEG3)-Cy3 is a useful component for constructing custom fluorescent probes and modular reagent libraries where a Cy3 fluorophore must be installed onto defined scaffolds. Chemical biology teams leverage the azide handle to assemble Cy3-containing probes from alkyne-functional recognition elements, linkers, or surface-reactive materials, enabling rapid generation of labeled constructs for fluorescence imaging and assay screening. This approach is particularly valuable when probe architecture needs to be varied systematically while keeping the fluorophore constant, such as during optimization of labeling density, linker length, or conjugate format for fluorescence readouts.