Post-synthetic modification of oligonucleotides containing 5-trifluoromethylpyrimidine bases

Abstract A practical and operationally simple post-synthetic modification of oligonucleotides containing 5-trifluoromethylpyrimidine bases is described. Trifluoromethyl group was used as a post-synthetic precursor and 5-trifluoromethylpyrimidine bases within oligonucleotides were converted into the corresponding 5-carboxy-, 5-cyano-, 5-amidinyl-, and 5-carbamoyl derivatives by treatment with an alkaline solution and amines. Moreover, post-synthetic treatment of fully protected and controlled pore glass (CPG)-attached oligonucleotides proceeded successfully with the simultaneous removal of all protecting groups, cleavage from CPG, and conversion of the trifluoromethyl group to afford the corresponding modified oligonucleotides.