Effects of acid-mediated deamination of cytidine and 5-methylcytidine on solid-phase synthesis of oligonucleotides

Oligonucleotide therapeutics have attracted considerable attention in recent years as a new drug discovery modality. They are generally produced via solid-phase oligonucleotide synthesis based on phosphoramidite chemistry. Oligonucleotide therapeutics form Watson–Crick base pairs with the target RNA and strictly recognize their sequence for gene regulation; therefore, structural changes in nucleobases could be crucial and should be avoided during oligonucleotide synthesis. In this study, we investigated the deamination of cytidine and 5-methylcytidine during the acid-mediated removal of dimethoxytrityl (DMTr) group of solid-phase oligonucleotide synthesis. Our results suggest that the deamination reaction proceeds regardless of the structure of the sugar moiety of the phosphoramidite monomer, particularly in reaction systems containing more than 1 % of water. The data from this study is believed highly beneficial and helpful for avoiding acid-mediated deamination of cytidine and 5-methylcytidine during oligonucleotide synthesis.