Small-molecule-catalysed deamination enables transcriptome-wide profiling of N⁶-methyladenosine in RNA

The deamination reaction is important to both fundamental organic chemistry and biochemistry. Traditional chemical methods of deamination rely on the use of aryldiazonium salts under harsh acidic conditions, which limits the application scope for most biological substrates. Here we present an N-nitrosation strategy for deamination under mild conditions that DNA and RNA biological macromolecules can tolerate. Cooperative catalysis combining a carbonyl organocatalyst with a Lewis acid catalyst facilitates the formation of a carbon-nitro intermediate from a primary amine, which, on rearrangement into N-nitrosamine, leads to the selective deamination of unsubstituted canonical DNA/RNA bases under mild conditions. We used this approach to deaminate adenine into hypoxanthine, read as guanine by reverse transcriptases or DNA polymerases, while N⁶-methyladenosine sites resist deamination and remain identified as adenine. This reactivity enables a chemically mild, low-input detection method for sequencing of adenosine methylation at base resolution, named chemical cooperative catalysis-assisted N⁶-methyladenosine sequencing.