New synthetic route to ethynyl-dUTP: A means to avoid formation of acetyl and chloro vinyl base-modified triphosphates that could poison SELEX experiments

Pascal Röthlisberger (1) , Fabienne Levi-Acobas (1) , Marcel Hollenstein (1)

1 Chimie bioorganique des acides nucléiques - Bioorganic chemistry of nucleic acids

5-Ethynyl-2'-deoxyuridine is a common base-modified nucleoside analogue that has served in various applications including selection experiments for potent aptamers and in biosensing. The synthesis of the corresponding triphosphates involves a mild acidic deprotection step. Herein, we show that this deprotection leads to the formation of other nucleoside analogs which are easily converted to triphosphates. The modified nucleoside triphosphates are excellent substrates for numerous DNA polymerases under both primer extension and PCR conditions and could thus poison selection experiments by blocking sites that need to be further modified. The formation of these nucleoside analogs can be circumvented by application of a new synthetic route that is described herein.

Keywords: In vitro selection; Nucleobase modification; Nucleoside triphosphates; PCR; Primer extension

Domains: Chemical Sciences; Chemical Sciences; Organic chemistry

Pascal Röthlisberger, Fabienne Levi-Acobas, Marcel Hollenstein. New synthetic route to ethynyl-dUTP: A means to avoid formation of acetyl and chloro vinyl base-modified triphosphates that could poison SELEX experiments. Bioorganic and Medicinal Chemistry Letters, 2017, 27 (4), pp.897-900. ⟨10.1016/j.bmcl.2017.01.009⟩. ⟨pasteur-02012264⟩