Fluorogenic labeling of 5-formylpyrimidine nucleotides in DNA and RNA.

Samanta, B.; Seikowski, J.; Höbartner, C.

doi:10.1002/anie.201508893

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Fluorogenic labeling of 5-formylpyrimidine nucleotides in DNA and RNA.

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Samanta, B.
Research Group of Nucleic Acid Chemistry, MPI for Biophysical Chemistry, Max Planck Society;

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Seikowski, J.
Research Group of Nucleic Acid Chemistry, MPI for Biophysical Chemistry, Max Planck Society;

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Höbartner, C.
Research Group of Nucleic Acid Chemistry, MPI for Biophysical Chemistry, Max Planck Society;

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Citation

Samanta, B., Seikowski, J., & Höbartner, C. (2016). Fluorogenic labeling of 5-formylpyrimidine nucleotides in DNA and RNA. Angewandte Chemie International Edition, 55(5), 1912-1916. doi:10.1002/anie.201508893.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0029-C38E-1

Abstract

5-Formylcytosine (5fC) and 5-formyluracil (5fU) are natural nucleobase modifications that are generated by oxidative modification of 5-methylcytosine and thymine (or 5-methyluracil). Herein, we describe chemoselective labeling of 5-formylpyrimidine nucleotides in DNA and RNA by fluorogenic aldol-type condensation reactions with 2,3,3-trimethylindole derivatives. Mild and specific reaction conditions were developed for 5fU and 5fC to produce hemicyanine-like chromophores with distinct photophysical properties. Residue-specific detection was established by fluorescence readout as well as primer-extension assays. The reactions were optimized on DNA oligonucleotides and were equally suitable for the modification of 5fU- and 5fC-modified RNA. This direct labeling approach of 5-formylpyrimidines is expected to help in elucidating the occurrence, enzymatic transformations, and functional roles of these epigenetic/epitranscriptomic nucleobase modifications in DNA and RNA.