A practical dinucleotide phosphoramidite chemistry for de novo DNA synthesis via block coupling

Abstract

With the development of synthetic biology, the demand for high-quality long oligonucleotides is increasing. The use of dinucleotide phosphoramidites (dimer amidites) will reduce half of the steps required in the stepwise monomer condensation, which is expected to lead to the high-quality synthesis of oligonucleotides. Herein, we report a convenient, unified procedure for the sustainable preparation of fully protected dimer amidites bearing a methyl phosphate and a β-cyanoethyl phosphoramidite. Key precursors of those amidites—dimers containing a 3′-hydroxyl group—have been prepared in high yield using a one-pot, scalable approach. The structures of all 16 dimer amidites and corresponding 3ʹ-hydroxyl dimers were confirmed by HPLC-MS and 31P NMR spectra. With these dimer amidites, modification of the standard method for automated solid-phase oligonucleotide synthesis enables high-yield block couplings. Oligonucleotides synthesized following this method are of sufficient quality to assemble gene-length DNA fragments. As a consequence, we develop a practical dinucleotide phosphoramidite chemistry for de novo DNA synthesis.