Versatile H-Phosphonate Platform for Backbone-Modified Dinucleotide Blockmers Enabling Oligonucleotide SAR

Abstract Oligonucleotides are an emerging therapeutic modality with the unique ability to modulate disease-associated proteins at the genetic level. Backbone modifications are critical for improving drug-like properties of oligonucleotides, yet no general platform exists for the modular synthesis of diverse backbone-modified oligonucleotide blockmers; current approaches require air/moisture-sensitive P(III) reagents and are each tailored to a specific modification type. To expand access to unusual backbone-modified oligonucleotides, we developed dinucleotide blockmers containing chemically modified phosphates that are suitable for assembly into longer oligonucleotides through solid-phase methods. Our methods exploit the ambiphilic reactivity of H-phosphonate diester dinucleotide blockmers, providing access to unconventional oligonucleotides bearing backbone modifications ranging from alkyl groups to sulfonamides without air/moisture-sensitive intermediates or hazardous reagents. These methods are expected to enable backbone structure–activity relationship studies in oligonucleotide discovery chemistry, offering a scalable and robust route for rapid analog generation.