Chemical Conversion of 5‐Fluoromethyl‐ and 5‐Difluoromethyl‐Uracil Bases in Oligonucleotides Using Postsynthetic Modification Strategy

Abstract

AbstractThis article describes the postsynthetic modification of oligonucleotides (ONs) containing 2′‐deoxy‐5‐fluoromethyluridine (dUCH2F) and 2′‐deoxy‐5‐difluoromethyluridine (dUCHF2). Reactions of fully protected and controlled pore glass (CPG)‐attached ONs containing dUCH2F and dUCHF2 in basic solutions result in deprotection of all protecting groups except for the 4,4′‐dimethoxytrityl group, cleavage from CPG, and conversion of the fluoromethyl or difluoromethyl groups to afford the corresponding ONs containing 5‐substituted 2′‐deoxyuridines. Moreover, the difluoromethyl group can be converted to formyl, oxime, or hydrazone via the postsynthetic conversion of protection‐ and CPG‐free ON containing dUCHF2. © 2023 Wiley Periodicals LLC.Basic Protocol 1: Synthesis of fully protected and CPG‐attached oligonucleotides containing 2′‐deoxy‐5‐fluoromethyluridine and 2′‐deoxy‐5‐difluoromethyluridineBasic Protocol 2: Postsynthetic modification of fully protected and CPG‐attached oligonucleotides containing 2′‐deoxy‐5‐fluoromethyluridineBasic Protocol 3: Postsynthetic modification of fully protected and CPG‐attached oligonucleotide containing 2′‐deoxy‐5‐difluoromethyluridineBasic Protocol 4: Postsynthetic modification of protection‐ and CPG‐free oligonucleotide containing 2′‐deoxy‐5‐difluoromethyluridineSupport Protocol: Synthesis of 2′‐deoxy‐5‐fluoromethyluridine and 2′‐deoxy‐5‐difluoromethyluridine phosphoramidites