Development of Silyl-Protected Phosphoramidite Building Blocks for Short ssDNA Synthesis†

Abstract

To overcome the depurination challenges associated with classical DNA synthesis methods, this study introduces a novel approach using fluoride-sensitive, triisopropylsilyl (TIPS)-protected phosphoramidite monomers for the efficient synthesis of short single-stranded DNA. The bulky TIPS group selectively protects the 5'-hydroxyl group of nucleosides and can be rapidly removed under mild, non-acidic conditions using fluoride ions, minimizing side reactions. Four novel TIPS-protected phosphoramidite monomers were synthesized and characterized, achieving >99% deprotection efficiency. These monomers were applied to the solid-phase synthesis of a 5-mer ssDNA sequence, yielding an overall efficiency of 99% for each cycle. The strategy demonstrates significant potential for improving the reliability and scalability of oligonucleotide synthesis, offering a promising alternative for applications in synthetic biology and nucleic acid research.