Preparation of Boranophosphate DNA via the Boranophosphotriester Method and Synthesis of P-modified DNAs from Boranophosphate DNA via an Acyl Phosphite Intermediate

Boranophosphate DNAs, in which one of the nonbridging oxygen atoms in the phosphate moiety is replaced with a borano group, are promising antisense oligonucleotide candidates because of their high nuclease resistance and low cytotoxicity. In Basic Protocol 1, we describe the synthesis of a dithymidylate boranophosphodiester via a boranophosphotriester method. Using the boranophosphotriester method, the condensation of a deoxyribonucleoside 3’-O-boranophosphodiester, which contains a borano group with a 5’-hydroxy group of another deoxyribonucleoside, followed by the deprotection of a protecting group at the phosphorus center, is conducted to yield a boranophosphodiester. A boranophosphodiester is also a useful synthetic precursor, and several P-modified nucleic acid derivatives can be successfully synthesized via the conversion reaction of a boranophosphodiester. In Basic Protocol 2, we describe the conversion reaction of the boranophosphodiester through an acyl phosphite intermediate. During the conversion reaction, various P-modified nucleic acid derivatives, such as a phosphorothioate diester, phosphotriester, phosphoramidate, phosphorothioate triester, and phosphorothioamidate, are obtained in good yields (69% to 93%). © 2025 Wiley Periodicals LLC.

Basic Protocol 1: Synthesis of dithymidylate boranophosphodiester

Support Protocol 1: Preparation of 3-[(trimethylsilyl)oxy]propanenitrile

Support Protocol 2: Preparation of PyNTP

Support Protocol 3: Preparation of compound 7

Basic Protocol 2: One-pot synthesis of P-modified nucleic acid derivatives