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Nucleic Acids Research Advance Access originally published online on January 12, 2009
Nucleic Acids Research 2009 37(5):1477-1485; doi:10.1093/nar/gkn1066
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Nucleic Acids Research, 2009, Vol. 37, No. 5 1477-1485
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Chemistry and Synthetic Biology

Diene-modified nucleotides for the Diels–Alder-mediated functional tagging of DNA

Vinciane Borsenberger and Stefan Howorka*

Department of Chemistry, Institute of Structural Molecular Biology, University College London, London WC1H 0AJ, UK

*To whom correspondence should be addressed. Tel: +44 20 7679 4702; Fax: +44 20 7679 7463; Email: s.howorka{at}ucl.ac.uk

Received July 23, 2008. Revised December 16, 2008. Accepted December 18, 2008.

We explore the potential of the Diels–Alder cycloaddition for the functional tagging of DNA strands. A deoxyuridine triphosphate derivative carrying a diene at position 5 of the pyrimidine base was synthesized using a two-step procedure. The derivative was efficiently accepted as substrate in enzymatic polymerization assays. Diene carrying strands underwent successful cycloaddition with maleimide-terminated fluorescence dyes and a polymeric reagent. Furthermore, a nucleotide carrying a peptide via a Diels–Alder cyclohexene linkage was prepared and sequence-specifically incorporated into DNA. The Diels–Alder reaction presents a number of positive attributes such as good chemoselectivity, water compatibility, high-yield under mild conditions and no additional reagents apart from a diene and a dienophile. Furthermore, suitable dienophiles are commercially available in the form of maleimide-derivatives of fluorescent dyes and bioaffinity tags. Based on these advantages, diene- and cyclohexene-based nucleotide triphosphates are expected to find wider use in the area of nucleic acid chemistry.


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