N-methyl-N'-methyl-O-(m-PEG4)-O'-(azide-PEG4)-Cy3 | CAS 2107273-64-1

N-methyl-N'-methyl-O-(m-PEG4)-O'-(azide-PEG4)-Cy3 is a Cy3-based fluorescent conjugation reagent bearing an azide-PEG4 handle for downstream click chemistry labeling. The PEG spacers are designed to reduce steric constraints during bioconjugation, enabling controlled attachment of the Cy3 fluorophore to biomolecules, peptides, and surfaces that carry complementary cyclooctyne/alkyne click partners. Its orange-red emission makes it a widely used option for fluorescence microscopy and flow cytometry workflows where Cy3-compatible filter sets are available.

1. Biomolecule Click Labeling

N-methyl-N'-methyl-O-(m-PEG4)-O'-(azide-PEG4)-Cy3 is used to generate fluorescently tagged proteins, peptides, and other biomolecules via azide-alkyne click bioconjugation. Researchers incorporate the reagent into labeling schemes to attach Cy3 to targeting ligands, affinity reagents, or carrier proteins while leveraging the PEG spacers to maintain fluorophore accessibility and reduce aggregation-driven signal artifacts. This format is particularly common in chemical biology labs developing fluorescent conjugates for imaging, binding studies, and reagent validation.

2. Fluorescence Microscopy Tracing

N-methyl-N'-methyl-O-(m-PEG4)-O'-(azide-PEG4)-Cy3 supports fluorescence microscopy experiments that track labeled biomolecular assemblies, cell-associated probes, or surface-bound constructs after click attachment. The Cy3 fluorophore is frequently selected for multicolor imaging panels where its emission can be separated from common green and far-red channels using standard microscope filter sets. By using the azide-functional PEG handle for conjugation, investigators can prepare consistent fluorescent labeling reagents for fixed-cell studies, co-localization experiments, and qualitative localization mapping.

3. Flow Cytometry Conjugate Preparation

N-methyl-N'-methyl-O-(m-PEG4)-O'-(azide-PEG4)-Cy3 is commonly used in flow cytometry reagent development to produce Cy3-labeled biomolecules for cell staining and binding readouts. The azide group enables click-based attachment to cyclooctyne/alkyne-functional ligands or carriers, supporting streamlined generation of fluorescent conjugates used for screening labeling conditions and comparing probe lots. PEG spacing helps maintain labeling uniformity and reduces steric effects that can otherwise influence conjugate binding to cell-surface targets.

4. Surface and Hydrogel Functionalization

N-methyl-N'-methyl-O-(m-PEG4)-O'-(azide-PEG4)-Cy3 is applied in biomaterials research to fluorescently functionalize surfaces, coatings, and hydrogel matrices through click-compatible immobilization strategies. Material scientists use the azide-PEG4 handle to incorporate Cy3 into polymer networks or onto functionalized substrates, enabling visualization of material distribution, coating integrity, and biomolecule-material interactions. This approach is frequently used when a stable, covalently attached fluorescent tag is required for imaging-based characterization of engineered interfaces.