N-(Azide-PEG3)-N'-(PEG4-acid)-Cy5
CAS No.: 2107273-42-5
Cat No.: BP-501679
Purity: 96%
4.5 
N-(Azide-PEG3)-N'-(PEG4-acid)-Cy5 is a heterobifunctional, PEG-based Cy5 conjugate that combines a terminal azide handle with a carboxylic acid–terminated PEG spacer, providing a flexible, water-soluble scaffold for modular PROTAC and targeted degradation workflows. The PEG3 segment introduces an azide functional group suitable for bioorthogonal conjugation (e.g., copper-free or copper-catalyzed azide–alkyne cycloaddition) to attach the Cy5-containing moiety to a complementary linker or targeting element, while the PEG4-acid segment offers a negatively charged, hydrophilic terminus that can be used for amide coupling or salt-forming strategies during PROTAC assembly. In targeted protein degradation research, this type of linker enables incorporation of a fluorescent reporter into otherwise complex degraders, facilitating synthesis verification, cellular uptake/trafficking studies, and monitoring of degrader localization without substantially perturbing binding due to the spacer-mediated separation. Its dual-reactivity and tunable spacing make it valuable for constructing imaging-compatible PROTACs and for optimizing conjugation chemistry in experimental degradation pipelines.
Structure of 2107273-42-5
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This N-(Azide-PEG3)-N'-(PEG4-acid)-Cy5 linker is designed to support modular PROTAC assembly by providing orthogonal reactive handles and a flexible polyethylene glycol (PEG) scaffold. Its azide functionality enables bioorthogonal conjugation, while the terminal acid group supports coupling strategies to attach targeting ligands. The Cy5 label further facilitates analytical tracking of linker incorporation and construct integrity. Detailed structural and reactivity considerations are provided below.
Structure: The molecule comprises a Cy5 fluorophore connected through PEG spacers to an azide-bearing terminus and a terminal carboxylic acid. It contains an organic azide, ether linkages within PEG chains, and a carboxylic acid suitable for amide formation. The flexible PEG segments enhance solubility and reduce steric constraints.
Reactivity: The azide group is compatible with copper-free or copper-catalyzed azide–alkyne cycloaddition for attaching alkyne-functional partners under mild conditions. The terminal acid can be activated for coupling to amine-bearing ligands using standard carbodiimide/activator chemistries to form stable amide bonds. Typical solvents include polar aprotic media or aqueous buffers compatible with PEG stability, with reaction temperatures and pH selected to preserve functional groups and maintain linker integrity.
* 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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