N,N′-bis-(azide-PEG3)-Cy5 is a Cy5-based fluorescent linker bearing two terminal azide groups separated by short, three–ethylene glycol (PEG3) spacers. Structurally, the dye core provides strong excitation/emission for optical tracking, while the azide termini enable bioorthogonal conjugation via azide–alkyne cycloaddition (CuAAC or strain-promoted variants), allowing modular attachment to PROTAC scaffolds or targeting ligands. In targeted protein degradation workflows, this type of linker is valuable for constructing degraders with defined stoichiometry and for incorporating fluorescent handles that report on synthesis yield, cellular uptake, and intracellular localization without requiring protein-specific labeling. The PEG spacers help reduce steric hindrance and can improve accessibility of the reactive azide groups during conjugation. Researchers can use it to generate fluorescently traceable PROTAC intermediates and to support mechanistic studies of ternary complex formation and trafficking by correlating degradation activity with dye distribution.
Structure of 2107273-46-9
* For research and manufacturing use only. Not for human or clinical use.
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This N,N'-bis-(azide-PEG3)-Cy5 linker is a multifunctional, azide-bearing PEG–Cy5 conjugate designed for modular PROTAC construction and subsequent bioconjugation workflows. Its azide handles enable efficient, orthogonal click-type coupling to complementary partners, while the PEG spacer supports solubility and flexible presentation of reactive groups. The Cy5 fluorophore further facilitates tracking of conjugation efficiency and monitoring of linker incorporation in targeted protein degradation experiments.
Structure: The molecule contains a Cy5 chromophore connected through PEG-based spacers to two terminal azide groups. It features ether-rich PEG segments, aromatic and polymethine components typical of cyanine dyes, and azide functional groups suitable for bioorthogonal ligation. The overall structure promotes aqueous compatibility and conformational flexibility.
Reactivity: The azide termini are compatible with copper-catalyzed azide–alkyne cycloaddition and strain-promoted azide–alkyne cycloaddition, enabling formation of stable triazole linkages under commonly used click chemistry conditions. Typical approaches employ inert atmosphere or oxygen-tolerant variants where necessary, with solvents such as aqueous buffers mixed with suitable organic co-solvents to maintain solubility. Reaction design should prioritize orthogonality with other functional groups on PROTAC building blocks and verify completeness by fluorescence or analytical methods.
* 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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