N-(m-PEG9)-N'-(propargyl-PEG8)-Cy5
CAS No.: 2107273-10-7
Cat No.: BP-501144
4.5 
N-(m-PEG9)-N'-(propargyl-PEG8)-Cy5 is a heterobifunctional PEG–dye linker that combines a Cy5 fluorophore with two polyethylene glycol chains connected through an amide-bearing junction, providing a flexible, water-soluble handle for PROTAC workflows. Structurally, it features a terminal propargyl group on one PEG segment that enables copper-catalyzed azide–alkyne cycloaddition (CuAAC) for orthogonal conjugation, while the Cy5 moiety offers sensitive fluorescence for tracking compound uptake, cellular localization, and degradation-associated binding events. In PROTAC design, this linker can be used to functionalize one end of a bifunctional construct (e.g., for attaching to an azide-functional ligand or warhead) without perturbing the binding pharmacophores, as the PEG spacers help reduce steric hindrance and nonspecific interactions. Its value lies in enabling real-time experimental readouts and mechanistic studies of targeted protein degradation conjugates, including synthesis verification and imaging-guided optimization of linker length and attachment chemistry.
Structure of 2107273-10-7
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This PROTAC linker reagent, N-(m-PEG9)-N'-(propargyl-PEG8)-Cy5, provides a flexible, water-compatible polyethylene glycol (PEG) architecture for building distance-tunable conjugates in targeted protein degradation workflows. Its dual functional design supports orthogonal bioconjugation strategies, enabling controlled attachment of targeting ligands and payload handles while maintaining solubility and reducing nonspecific interactions. The following sections describe the linker’s structural features and practical reactivity considerations for PROTAC assembly.
Structure: The linker comprises two PEG segments flanking a Cy5 fluorophore, connected through amide linkages and terminated with a propargyl (alkyne) handle. The PEG chains confer hydrophilicity and conformational flexibility, while the Cy5 core provides a stable, conjugatable chromophore suitable for tracking conjugate formation.
Reactivity: The terminal propargyl group is designed for copper-catalyzed azide–alkyne cycloaddition or related click-type conjugation chemistries, typically requiring an azide partner on the PROTAC components. Reactions are commonly performed in polar organic/aqueous mixtures under conditions that support alkyne activation while preserving PEG solubility. Mild bases and standard CuAAC ligand systems are often used to improve rate and minimize side reactions, enabling efficient modular assembly of PROTAC constructs.
* 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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