Construction of Pyrimidine Bases Bearing Carboxylic Acid Equivalents at the C5 Position by Postsynthetic Modification of Oligonucleotides

Abstract

This unit describes postsynthetic modification of oligonucleotides (ONs) containing 2′‐deoxy‐5‐trifluoromethyluridine and 2′‐deoxy‐5‐trifluoromethylcytidine. In ONs, the trifluoromethyl group at the C5 position of pyrimidine bases is converted into a variety of carboxylic acid equivalents using alkaline and amine solutions. In addition, treating fully protected and controlled pore glass (CPG)‐attached ONs with methylamine and sodium hydroxide aqueous solution results in deprotection of all protecting groups (except the 4,4′‐dimethoxytrityl group), cleavage from CPG, and simultaneous conversion of the trifluoromethyl group to afford the corresponding ONs containing 5‐substituted pyrimidine bases. © 2019 by John Wiley & Sons, Inc.

Synthesis of fluorescent 5-heteroarylpyrimidine-containing oligonucleotides via post-synthetic trifluoromethyl conversion

“…Our group recently reported that mono-, di-, and tri-fluoromethyl groups at the C5 position of pyrimidine bases can be used as precursors for post-synthetic modification. [32][33][34][35] For example, treating ONs containing 5-trifluoromethyluracil (U CF3 ) and 5-trifluoromethylcytosine (C CF3 ) with alkaline and amine solution resulted in the conversion of trifluoromethyl (CF 3 ) group into carboxylic acid equivalents (Scheme 1c). 32,33 Leszczynska et al also applied this 5-CF 3 conversion for the synthesis of C5-modified pyrimidine ribonucleosides.…”

“…[32][33][34][35] For example, treating ONs containing 5-trifluoromethyluracil (U CF3 ) and 5-trifluoromethylcytosine (C CF3 ) with alkaline and amine solution resulted in the conversion of trifluoromethyl (CF 3 ) group into carboxylic acid equivalents (Scheme 1c). 32,33 Leszczynska et al also applied this 5-CF 3 conversion for the synthesis of C5-modified pyrimidine ribonucleosides. 36,37 Concerning the CF 3 group conversion, it has been reported that the CF 3 group on the aromatic ring can be converted into nitrogen-containing heterocycles.…”

Synthesis of Nucleotides Bearing the 2′‐O‐Trifluoromethyl Group and Their Application in RNA Analogs Preparation

“…The two fluorine modifications combined with the natural phosphate backbone exhibited significant thermal stability of hybridization to RNA relative to the first‐generation DNA phosphorothioates (PS‐DNA) but with insufficient protection against degradation by nucleases (Egli et al., 2005). For nucleobase modification, the synthesis of 5‐fluoromethyluridine, difluoromethyluridine and trifluoromethylated purine route and their application has been demonstrated, respectively (Chrominski et al., 2020; Ito et al., 2023). The trifluoromethoxy group (‐OCF 3 ) has received growing interest over the past few years due to its specific electronic properties (Hammett constants: σ p = 0.35, σ m = 0.38; Swain–Lupton constants: F = 0.39, R = ‐0.04) (C. Hansch et al., 1991), remarkable lipophilicity (Hansch parameter: π R = 1.04) (Leo et al., 1971; Hansch & Leo, 1979; Hoekman, 1996; Leroux et al., 2008;), and robust resistance to metabolic degradation (Hagmann, 2008; Meanwell, 2011).…”