N-methyl-N'-methyl-O-(m-PEG4)-O'-(propargyl-PEG4)-Cy3
CAS No.: 2107273-62-9
Cat No.: BP-500605
Purity: 95%
4.5 
N-methyl-N'-methyl-O-(m-PEG4)-O'-(propargyl-PEG4)-Cy3 is a Cy3-derived fluorescent PROTAC linker that combines a cyanine dye with two PEG4-based ether segments and a terminal propargyl handle. Structurally, it is characterized by an O-alkylated PEG architecture that provides aqueous solubility and conformational flexibility, while the propargyl group enables bioorthogonal conjugation via copper-free azide–alkyne cycloaddition to attach the dye-containing fragment to azide-functionalized targeting ligands or handles. In PROTAC workflows, this linker is used to generate fluorescently traceable conjugates, allowing researchers to monitor synthesis efficiency, verify cellular uptake, and track subcellular localization of degradation constructs without substantially perturbing linker hydrophilicity. Its PEG spacers help reduce nonspecific interactions and improve compatibility with linker–ligand geometries commonly used in targeted protein degradation studies, supporting quantitative imaging and mechanistic experiments that benefit from real-time visualization.
Structure of 2107273-62-9
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This PROTAC linker is engineered to connect a targeting ligand to a degraders’ recruitment module while incorporating a Cy3-compatible fluorescent handle for monitoring and characterization. Its PEG-based, ether-rich architecture supports water solubility and flexible spacing, which can improve effective ternary complex formation. The molecule is well suited for experimental PROTAC synthesis and subsequent analytical tracking;
Structure: The linker contains multiple ether linkages within PEG segments and terminal functional groups designed for conjugation. It features a propargyl moiety for click-type coupling and a Cy3-compatible connectivity pattern, with N-methylated nitrogen atoms contributing to overall stability and controlled polarity.
Reactivity: The propargyl functionality enables copper-catalyzed azide–alkyne cycloaddition for efficient, chemoselective “click” conjugation to azide-bearing PROTAC components. Typical approaches use a Cu(I) source generated in situ, with appropriate ligands to minimize side reactions, and polar organic/aqueous solvent mixtures to maintain solubility. Reaction progress can be monitored by fluorescence when Cy3 is present, and purification is commonly performed by chromatography to remove residual catalysts and unreacted partners.
* Our calculator is based on the following equation:
Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C1V1 = C2V2
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