Quick Access to Nucleobase-Modified Phosphoramidites for the Synthesis of Oligoribonucleotides Containing Post-Transcriptional Modifications and Epitranscriptomic Marks

Herein, we report a straightforward one-step procedure for modifying N-nucleophilic groups in the nucleobases of commercially available nucleoside phosphoramidites. This method involves the deprotonation of amide groups under phase-transfer conditions and subsequent reaction with electrophilic molecules such as alkyl halides or organic isocyanates. Using this approach, we obtained 10 different classes of modified nucleoside phosphoramidites suitable for the synthesis of oligonucleotides, including several noncanonical nucleotides found in natural RNA or DNA (e.g., m(6)A, i(6)A, m(1)A, g(6)A, m(3)C, m(4)C, m(3)U, m(1)G, and m(2)G). Such modification of nucleobases is a common mechanism for post-transcriptional regulation of RNA stability and translational activity in various organisms. To better understand this process, relevant cellular recognition partners (e.g., proteins) must be identified and characterized. However, this step has been impeded by limited access to molecular tools containing such modified nucleotides.

Automated summary

The study presents a method for modifying nucleobases in nucleoside phosphoramidites, resulting in 10 different classes of modified nucleoside phosphoramidites suitable for oligonucleotide synthesis, including noncanonical nucleotides found in natural RNA or DNA. This approach can help in understanding the post-transcriptional regulation of RNA stability and translational activity. Further research requires identification and characterization of relevant cellular recognition partners, though limited access to molecular tools with modified nucleotides remains a challenge.