Product of the Month: Dde-based Linkers

Product of the Month: Dde-based Linkers

Published on 30/07/2020

Placing Dde as one terminal group of a linker and a functional group prone for conjugation as the other or using Dde as the central connective portion of a linker, allows for the creation of new bifunctional linkers.

The use of linkers to join two chemical moieties requires their chemical stability towards various conditions as well as an established breaking point which allows for cleavage of the linker. Dde [N-1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)-3-ethyl] has been introduced as protecting group with cleavage conditions orthogonal to Fmoc/tBu protocols, thus being stable towards denaturing washing as well as acidic and basic conditions. Advantageously, the cleavage of Dde using a (buffered) aqueous solution of hydrazine or hydroxylamine can be followed spectrophotometrically due to the formation of a chromophoric product.

Dde-based linkers can selectively and temporarily be attached to:

  • Appropriately modified biomolecules for binding to streptavidin (with terminal biotin) (A), or conjugation to any solid supports, e.g. via Click reaction (B).
  • Solubilizing tags, e.g. hexa-lysine (“helping-hand linkers”, (C)), oligo-arginine, PEGs (D) or other hydrophilic groups improving the solubility of hydrophobic peptides or other compounds when being attached to either the N-terminus or any lysine side chain within a peptide sequence thus facilitating the handling and purification of insoluble and aggregation-prone peptides.
  • Dyes and any other conjugate for monitoring, diagnostics, targeting or other purposes.

Please click here to see various examples for Dde-based linkers on our Website.

Dde-based linkers

Dde-based linkers can be utilized for various applications: Attachment of a cleavable biotin tag to proteins for catch-and-release affinity purification over Streptavidin beads (A), reversible labeling or conjugation to other biomolecules, or reversible immobilization on solid supports via Click chemistry (B), temporary attachment of solubilizing tags like oligo-lysine (C) or PEGs (D).

Dde-based linkers with Dde as one of the terminal groups can be incorporated on-resin during SPPS in nearly quantitative steps after orthogonal deprotection of the N-terminus or any other sidechain amino function in the peptide sequence. Linkers with Dde as the connective element may be incorporated by means of their respective functional group(s). Dde can be selectively cleaved by using a (buffered) aqueous solution of hydrazine or hydroxylamine thus releasing the peptide after purification, streptavidin attachment, NCL-based assembly or any other reaction step. The cleavage can be monitored spectroscopically as the resulting pyrazole shows a strong absorption at 290 nm.

➔ Interested in further product details? Please get in contact for a Microsoft Teams product presentation!

➔ Related topics: “Peptide Easy Clean” for chromatography-free peptide purification – our Product of the Month in May 2020

➔ Please also see the Linkerology section on our webpage


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  • Synthesis of hydrophobic insulin-based peptides using a helping hand strategy; M. M. Disotuar, M. E. Petersen, J. M. Nogueira, M. S. Kay and D. H. Chou; Org Biomol Chem 2019; 17: 1703-1708.  
  • Chemical synthesis of Shiga toxin subunit B using a next-generation traceless "helping hand" solubilizing tag; J. M. Fulcher, M. E. Petersen, R. J. Giesler, Z. S. Cruz, D. M. Eckert, J. N. Francis, E. M. Kawamoto, M. T. Jacobsen and M. S. Kay; Org Biomol Chem 2019; 17: 10237-10244.
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  • Cleavable trifunctional biotin reagents for protein labelling, capture and release; Y. Yang and S. H. Verhelst; Chem Commun (Camb) 2013; 49: 5366-8.
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