N,N'-bis-(azide-PEG3)-Cy5

 CAS No.: 2107273-46-9  Cat No.: BP-500870  Purity: 98% 4.5  

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.

N,N'-bis-(azide-PEG3)-Cy5

Structure of 2107273-46-9

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Category
PROTAC Linker
Molecular Formula
C₄₁H₅₇ClN₈O₆
Molecular Weight
793.39

* For research and manufacturing use only. Not for human or clinical use.

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Popular Publications Citing BOC Sciences Products
Purity
98%
Solubility
DMSO, DMF, DCM, low solubility in water
Storage
Please store the product under the recommended conditions in the Certificate of Analysis.
Shipping
Room temperature in continental US; may vary elsewhere.
IUPACName
1-[2-[2-[2-(2-azidoethoxy)ethoxy]ethoxy]ethyl]-2-[(2E,4E)-5-[1-[2-[2-[2-(2-azidoethoxy)ethoxy]ethoxy]ethyl]-3,3-dimethylindol-1-ium-2-yl]penta-2,4-dienylidene]-3,3-dimethylindole;chloride
Excitation
649
Emission
667
InChI Key
ABWDMMSABAJXMT-UHFFFAOYSA-M
InChI
InChI=1S/C41H57N8O6.ClH/c1-40(2)34-12-8-10-14-36(34)48(20-24-52-28-32-54-30-26-50-22-18-44-46-42)38(40)16-6-5-7-17-39-41(3,4)35-13-9-11-15-37(35)49(39)21-25-53-29-33-55-31-27-51-23-19-45-47-43;/h5-17H,18-33H2,1-4H3;1H/q+1;/p-1
SMILES
CC1(C2=CC=CC=C2[N+](=C1C=CC=CC=C3C(C4=CC=CC=C4N3CCOCCOCCOCCN=[N+]=[N-])(C)C)CCOCCOCCOCCN=[N+]=[N-])C.[Cl-]
1. Impact of phospholipids on plasmid packaging and toxicity of gemini nanoparticles
Chilbert Dong, Ildiko Badea, Masoomeh Poorghorban, Ronald Verrall, Marianna Foldvari J Mater Chem B. 2015 Dec 7;3(45):8806-8822.doi: 10.1039/C5TB01400J.Epub 2015 Sep 29.
Understanding the relationship of structural modifications on the assembly and disassembly of synthetic or non-viral gene delivery is crucial with regard to their rational development. This study describes the use of fluorescence correlation spectroscopy (FCS), as a new tool, to investigate the effect of systematic chemical modifications to dicationic N,N-bis(dimethylalkyl)-α,ω-alkanediammonium surfactants (gemini surfactants) on the self-assembly and physical properties of a series of gemini nanoparticles (gemini NPs). A systematic screening of 27 gemini-plasmid (GP) complexes and gemini NPs showed that their final morphology is governed by the pre-compaction of plasmid by the gemini surfactants. The assembly process of gemini-plasmid intermediate complex (GP) and the final gemini NP (or gemini-plasmid-lipid complex, GPL) was monitored by the tracking of the Cy5-labeled plasmid. Based on diffusion properties, GP complexes were larger than gemini NPs (300-500 nm for GP and 200-300 nm for GPLs). Stoichiometric analysis of the raw intensity histograms showed that both GPs and GPLs particles were composed of multiple plasmids. The final GPLs contain fewer plasmids (2-20 per particle) compared to the intermediate GP (5-35 per particle). The addition of phospholipids dispersed and stabilized GPs to form GPL, but the type of phospholipid (DOPE or DD 1:3) had little effect on the final size of the particles. The FCS data were both validated and complemented by the results of studies of dynamic light scattering (DLS), atomic force microscopy (AFM), X-ray scattering and dye-exclusion assays. A model for gemini NP assembly involving supramolecular aggregate intermediates is proposed.

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.

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Concentration (start) x Volume (start) = Concentration (final) x Volume (final)
It is commonly abbreviated as: C1V1 = C2V2

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Tip: Chemical formula is case sensitive. C22H30N4O c22h30n40
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