N,N'-bis-(propargyl-PEG4)-Cy5
CAS No.: 2107273-08-3
Cat No.: BP-500342
Purity: 97%
4.5 
N,N’-bis-(propargyl-PEG4)-Cy5 is a Cy5-derived fluorescent linker bearing two terminal propargyl groups separated by two PEG4 chains, enabling efficient conjugation through copper-catalyzed azide–alkyne cycloaddition or related click chemistries. Structurally, the molecule combines a near-infrared cyanine dye core with polyethylene glycol spacers that provide aqueous solubility and flexible distance control between the dye and the reactive handles. In PROTAC and targeted protein degradation workflows, such linkers are valuable for constructing fluorescently traceable degraders or for attaching reporter tags to either the ligand-binding module or the E3-recruiting module without substantially perturbing binding, because the PEG spacers can reduce steric interference and promote productive ternary complex formation. The dual propargyl functionality supports modular synthesis, allowing researchers to label intermediates, monitor conjugation efficiency, and track cellular uptake and intracellular localization in degradation studies.
Structure of 2107273-08-3
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This PROTAC linker reagent, N,N'-bis-(propargyl-PEG4)-Cy5, combines a PEG-based flexible spacer with two terminal propargyl handles for orthogonal conjugation and a Cy5 fluorophore for optical tracking. Its design supports efficient assembly of PROTAC constructs by enabling controlled attachment to targeting and recruiting ligands while preserving solubility and conformational adaptability. Detailed structural and synthetic guidance is provided below.
Structure: The molecule contains a PEG4-based bis-functional scaffold bearing two propargyl substituents, providing flexible ether-rich connectivity and terminal alkynes. The Cy5 moiety contributes a conjugated, dye-like aromatic system, while the overall framework includes ether linkages and amide-forming connectivity at the N,N′ positions.
Reactivity: The terminal alkynes are suitable for copper-catalyzed azide–alkyne cycloaddition or strain-promoted azide–alkyne cycloaddition, enabling modular PROTAC build strategies with azide-functional ligands. Typical coupling is performed under inert or oxygen-controlled conditions, using appropriate Cu(I) sources and stabilizing ligands for the copper route, or using catalyst-free conditions for the strain-promoted route. Solvent systems commonly favor polar organic media to maintain PEG solubility and reaction homogeneity.
* 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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