endo-BCN-PEG6-Boc
Cat No.: BP-501912
4.5 
Endo-BCN-PEG6-Boc is a bioorthogonal, BCN (bicyclononyne)–functionalized polyethylene glycol linker bearing a terminal Boc-protected group, designed for PROTAC and targeted protein degradation workflows that require efficient conjugation under mild conditions. The BCN moiety enables strain-promoted azide–alkyne cycloaddition (SPAAC) with azide-bearing partners without added catalysts, allowing rapid covalent attachment to PROTAC components such as ligands, handles, or affinity tags. The PEG6 spacer provides a flexible, hydrophilic chain that can reduce steric interference, improve solubility, and help preserve productive geometry for ternary-complex formation between the target-binding and E3-ligase-binding modules. In degradation research, this linker facilitates modular assembly and late-stage functionalization, supporting systematic optimization of linker length and attachment position to tune degradation potency and selectivity while maintaining experimental convenience.
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* For research and manufacturing use only. Not for human or clinical use.
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This endo-BCN-PEG6-Boc linker is designed for modular PROTAC synthesis, enabling efficient conjugation between targeting ligands and E3-recruiting moieties through bioorthogonal chemistry. Its PEG-based spacer promotes favorable solubility and conformational flexibility, while the endo-BCN handle supports strain-promoted cycloaddition with azide-bearing partners. The Boc-protected functionality provides a protected reactive site that can be unmasked under controlled conditions. Detailed structural and reactivity considerations are provided below.
Structure: The linker combines an endo-bicyclononyne (BCN) cyclooctyne core with a polyethylene glycol (PEG) spacer and a Boc-protected functional group. It contains multiple ether linkages characteristic of PEG, along with strained alkyne functionality enabling rapid cycloaddition. Overall polarity supports improved aqueous compatibility.
Reactivity: BCN-containing linkers typically react with azides via strain-promoted azide–alkyne cycloaddition, proceeding without added copper and generally under mild, aqueous-compatible conditions. For PROTAC assembly, the Boc group is commonly retained during coupling steps and then removed using acid-mediated deprotection to reveal the reactive handle for subsequent functionalization. Solvent systems that maintain solubility of both partners are preferred, and reaction progress is commonly monitored by analytical methods such as LC-MS.
* 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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