Oligonucleotide synthesis under mild deprotection conditions

• Published in: New journal of chemistry Vol. 47; no. 18; pp. 8714 - 8722
• Main Authors: Chillar, Komal, Eriyagama, Adikari M. D. N, Yin, Yipeng, Shahsavari, Shahien, Halami, Bhaskar, Apostle, Alexander, Fang, Shiyue
• Format: Journal Article
• Language: English
• Published: CAMBRIDGE Royal Soc Chemistry 09.05.2023; Royal Society of Chemistry
• Subjects: Aniline; Chemistry; Chemistry, Multidisciplinary; Nucleophiles; Nucleotides; Physical Sciences; Ribonucleic acid; RNA; Science & Technology; Synthesis; DNA ALKYLATION; OLIGODEOXYNUCLEOTIDES; GENE-REGULATION; N4-ACETYLCYTIDINE; RNA
• ISSN: 1144-0546; 1369-9261
• DOI: 10.1039/d2nj03845e

Over a hundred non-canonical nucleotides have been found in DNA and RNA. Many of them are sensitive toward nucleophiles. Because known oligonucleotide synthesis technologies require nucleophilic conditions for deprotection, currently there is no suitable technology for their synthesis. The recently disclosed method regarding the use of 1,3-dithian-2-yl-methyl (Dim) for phosphate protection and 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) for amino protection can solve the problem. With Dim-Dmoc protection, oligodeoxynucleotide (ODN) deprotection can be achieved with NaIO 4 followed by aniline. Some sensitive groups have been determined to be stable under these conditions. Besides serving as a base, aniline also serves as a nucleophilic scavenger, which prevents deprotection side products from reacting with ODN. For this reason, excess aniline is needed. Here, we report the use of alkyl Dim (aDim) and alkyl Dmoc (aDmoc) for ODN synthesis. With aDim-aDmoc protection, deprotection is achieved with NaIO 4 followed by K 2 CO 3 . No nucleophilic scavenger such as aniline is needed. Over 10 ODNs including one containing the highly sensitive N 4 -acetylcytidine were synthesized. Work on extending the method for sensitive RNA synthesis is in progress. The use of novel protecting groups makes it possible to incorporate sensitive epigenetically modified nucleosides such as N 4 -acetylcytidine into oligonucleotides.