Site-selective and rewritable labeling of DNA through enzymatic, reversible, and click chemistries

Andrew Wilkinson, Elodie Jagu, Krystian Ubych, Steven Coulthard, Ashleigh Rushton, Jack Kennefick, Qiang Su, Robert Neely, Francisco Fernandez-Trillo

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)
197 Downloads (Pure)

Abstract

Current methods for bioconjugation rely on the introduction of stable linkers that lack the required versatility to perform sequential functionalizations. However, sequential manipulations are an increasing requirement in chemical biology because they can underpin multiple analyses of the same sample to provide a wider understanding of cell behavior. Here, we present a new method to site-selectively write, remove, and rewrite chemical functionality to a biomolecule, DNA in this case. Our method combines the precision and robustness of methyltransferase-directed labeling with the reversibility of acyl hydrazones and the efficiency of click chemistry. Underpinning the method is a new S-adenosyl-l-methionine derivative to site-selectively label DNA with a bifunctional chemical handle containing an acyl hydrazone-linker and a terminal azide. Functional tags are conjugated via the azide and can be removed (i.e., untagged) when needed at the acyl hydrazone via exchange with hydroxyl amine. The formed hydrazide-labeled DNA is a versatile intermediate that can be either rewritten to reset the original chemical handle or covalently reacted with a permanent tag. This ability to write, tag, untag, and permanently tag DNA is exploited to sequentially introduce two fluorescent dyes on DNA. Finally, we demonstrate the potential of the method by developing a protocol to sort labeled DNA using magnetic beads, with subsequent amplification of the sorted DNA sample for further analysis. The presented method opens new avenues for site-selective bioconjugation and should underpin integrative approaches in chemical biology where sequential functionalizations of the same sample are required.
Original languageEnglish
Pages (from-to)525-534
Number of pages10
JournalACS Central Science
Volume6
Issue number4
Early online date27 Mar 2020
DOIs
Publication statusPublished - 22 Apr 2020

Bibliographical note

Funding Information:
The authors thank the University of Birmingham for the John Evans Fellowship to P.F.-T. and scholarships to A.W., K.U., A.E.R., and J.K. This work was supported by the European Union 634890, “BeyondSeq”, Royal Society U.K. (RG140613), the EPSRC (EP/N020901/1, EP/M506461/1), the Wellcome Trust (177ISSFPP), and the Birmingham Science City and the European Regional Development Fund. The authors thank Rachel O’Reilly for access to the ChemiDoc MP Imager and Tom Wilks for help with gel electrophoresis imaging. Finally, we thank both colleagues and Andrew Dove for critical reading of the manuscript and feedback.

Publisher Copyright:
Copyright © 2020 American Chemical Society.

Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.

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