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Nucleic Acids Res. 2009 Apr;37(5):1477-85. doi: 10.1093/nar/gkn1066. Epub 2009 Jan 12.

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

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


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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