N-Methyl-N'-(hydroxy-PEG2)-Cy5
CAS No.: 2107273-22-1
Cat No.: BP-501656
Purity: 98%
4.5 
N-Methyl-N'-(hydroxy-PEG2)-Cy5 is a Cy5-based fluorescent linker bearing a terminal hydroxy group and a short, two–ethylene glycol (PEG2) spacer. Structurally, it couples the polymethine dye core to a PEG2 chain through an N-methylated amide/urea-type linkage, providing a hydrophilic, flexible segment that improves aqueous solubility and helps reduce steric interference around the dye. In PROTAC and targeted-degradation workflows, such dye-linkers are commonly used as imaging or tracking modules to monitor conjugate integrity, cellular uptake, and intracellular trafficking, while the terminal hydroxy functionality enables downstream functionalization (e.g., conversion to activated derivatives for coupling to other PROTAC components). The PEG spacer’s conformational flexibility can also facilitate productive proximity between the labeled moiety and the binding partners during ternary complex formation. This product is therefore valuable for mechanistic studies and assay development in targeted protein degradation research where fluorescence readouts are required.
Structure of 2107273-22-1
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This N-Methyl-N'-(hydroxy-PEG2)-Cy5 linker is designed to integrate a Cy5 fluorophore into targeted protein degradation (PROTAC) constructs while providing a short, hydrophilic polyethylene glycol spacer for improved solubility and linker flexibility. Its functionalized termini enable reliable conjugation strategies used to assemble PROTACs and related bifunctional degraders. The following sections describe the structure and practical reactivity considerations in detail.
Structure: The linker contains a Cy5-derived chromophore bearing an N-methylated cyanine nitrogen substituent and a short hydroxy-terminated PEG spacer. It features ether linkages within the PEG segment, polar hydroxyl functionality, and aromatic/heteroaromatic regions characteristic of cyanine dyes, supporting strong fluorescence and enhanced aqueous compatibility.
Reactivity: Suitable PROTAC assembly typically relies on orthogonal functional-group chemistries that preserve dye integrity, such as amide coupling to an activated carboxylic acid partner or nucleophilic substitution/condensation at the hydroxyl- or amine-reactive handle, depending on the PROTAC warhead design. Mild, dye-compatible conditions are generally preferred; common approaches use carbodiimide-based coupling reagents or activated ester intermediates in polar aprotic or buffered solvents, with careful control of pH to minimize Cy5 photodegradation and side reactions.
* 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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