Oligonucleotide synthesis under mild deprotection conditions

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 NaIO4 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 NaIO4 followed by K2CO3. 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.

Automated summary

Over 100 non-canonical nucleotides have been discovered in DNA and RNA, many of which are sensitive to nucleophiles. However, the current oligonucleotide synthesis technologies require nucleophilic conditions for deprotection, making it unsuitable for their synthesis. A recently disclosed method using Dim for phosphate protection and Dmoc for amino protection has solved this problem. With this new protection method, deprotection can be achieved without the need for nucleophilic scavengers like aniline.