N1-methyladenosine detection with CRISPR-Cas13a/C2c2

Recent studies suggested that the widespread presence of N1-methyladenosine (m1A) plays a very important role in environmental stress, ribosome biogenesis and antibiotic resistance. The RNA-guided, RNA-targeting CRISPR Cas13a exhibits a “collateral effect” of promiscuous RNase activity upon target recognition with high sensitivity. Inspired by the advantage of CRISPR Cas13a, we designed a system to detect m1A induced mismatch, providing a rapid, simple and fluorescence-based m1A detection. For A-ssRNA, the Cas13a-based molecular detection platform showed a high fluorescence signal. For m1A-ssRNA, there is an about 90% decline of fluorescence. Moreover, this approach can also be used to quantify m1A in RNAs and applied for the analysis of dynamic m1A demethylation of 28S rRNA with AlkB.