Johannes Bingold, Erik Mafenbayer, Wibke Langenkamp, Lisa Liang, Chun Zhang, Malte Mildner, Julia Isabel Bahner, Mohamed Akmal Marzouk, Bettina Böttcher, Ann-Christin Pöppler, Ralf Weberskirch, Andreas Brunschweiger

Chemical Science 

DOI: 10.1039/d5sc06782k

Abstract

Chemical diversification of DNA-conjugated substrates is key in DNA-encoded library (DEL) synthesis and other nucleic acid-based technologies. One major challenge to the translation of synthesis methods to DNA-tagged substrates is the lack of solubility of the highly charged DNA oligomer in most organic solvents. A neutral acrylate block copolymer, devoid of any canonical nucleic acid-binding structure, tightly interacted with DNA oligonucleotides in their ammonium form, and solubilized them in nonpolar solvents such as dichloromethane, chloroform and toluene. The ternary DNA–copolymer–ammonium salt interactions led to the formation of aggregates in organic solvents whose size correlated with DNA oligomer length. This method for DNA solubilization was successfully applied to diversify DNA-tagged starting materials by three isocyanide multicomponent reactions (IMCR) with broad scope and excellent yields. The copolymer does not require tailored DNA conjugates and solubilized DNA oligomers of up to 80 nucleotides length. It will likely broaden the toolbox of DEL-compatible synthesis methods well beyond IMCR chemistry and it has application potential in other nucleic acid-based technologies that require a broadened solvent scope for nucleic acid conjugate synthesis.

Summary

This article presents a novel method for solubilizing DNA oligomers in organic solvents using a neutral acrylate block copolymer. The method leverages ternary interactions between the DNA, the copolymer, and ammonium salts to form aggregates in nonpolar solvents. This approach enables the use of DNA-tagged substrates in a variety of chemical reactions, including isocyanide multicomponent reactions (IMCR), which are typically challenging due to the poor solubility of DNA in organic solvents. The study demonstrates the successful application of this method to diversify DNA-tagged starting materials with excellent yields and broad scope, potentially expanding the range of DEL-compatible synthesis methods.

Highlights

1. A neutral acrylate block copolymer solubilizes DNA oligomers in nonpolar organic solvents.
2. Ternary interactions between DNA, copolymer, and ammonium salts form aggregates in organic solvents.
3. The method enables DNA-tagged substrates to undergo isocyanide multicomponent reactions (IMCR) with high yields.
4. DNA oligomers of up to 80 nucleotides length can be solubilized using this approach.
5. The copolymer system is compatible with downstream DEL operations such as enzymatic DNA tag ligation and barcode amplification.

Conclusion

The study introduces a conceptually novel approach to DNA solubilization in organic solvents using a neutral acrylate block copolymer. This method, termed CECOS (copolymer-mediated encoded chemistry in organic solvents), facilitates the translation of three isocyanide multicomponent reactions to DNA-tagged substrates with excellent yields and broad substrate scope. The copolymer system does not require tailored DNA barcodes or substrates and is compatible with various DNA barcoding strategies. This approach has the potential to significantly expand the range of DEL-compatible synthesis methods and may find applications in other nucleic acid-based technologies requiring a broader solvent scope. Future work will focus on further investigating the hydrophilic–lipophilic balance of the copolymer to improve understanding of the aggregate structure and potentially extend the solvent scope.