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Site-selective and Re-writable Labeling of DNA through Enzymatic, Reversible and Click Chemistries

preprint
revised on 31.01.2020 and posted on 03.02.2020 by Andrew A. Wilkinson, Elodie Jagu, Krystian Ubych, Steven Coulthard, Ashleigh E. Rushton, Jack Kennefick, Qiang Su, Robert K. Neely, Paco Fernandez-Trillo

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 re-write 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. un-tagged) when needed at the acyl hydrazone via exchange with hydroxyl amine. The formed hydrazide-labeled DNA is a versatile intermediate that can be either re-written to reset the original chemical handle, or covalently reacted with a permanent tag. This ability to write, tag, un-tag 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.

Funding

Royal Society (RG140613)

University of Birmingham

EPSRC (EP/N020901/1 and EP/M506461/1)

Wellcome Trust (177ISSFPP)

History

Email Address of Submitting Author

f.fernandez-trillo@bham.ac.uk

Institution

University of Birmingham

Country

United Kingdom

ORCID For Submitting Author

0000-0002-6680-5683

Declaration of Conflict of Interest

A.W., E. J., R.K.N. and P.F.-T. are named on a patent application (GB1913598.7) related to this work.

Version Notes

Resubmission

Exports