Mini crRNA-Mediated CRISPR/Cas12a System Enhanced Imaging of Multiple MicroRNAs in Cells

RNA imaging in live cells can provide comprehensive information on the expression, localization, degradation, storage, and regulation of RNA in cells, which is crucial for basic biology and clinical research. Our previous research finds that slicing the facilitated crRNA in the typical CRISPR/Cas12a system at a fitted site did not affect its <i>trans</i>-cleavage activity, which was previously reported to be triggered by targeted ssDNA or dsDNA, and a mini crRNA-mediated CRISPR/Cas12a (MCM-CRISPR/Cas12a) system was proposed. Here, we further apply it to enhanced imaging of MicroRNAs in cells by designing the activator in the system as a molecular beacon (MB), which can form a hybrid double-stranded structure of DNA/RNA with the targeted MicroRNA. When targeted MicroRNA is present, the hairpin structure of the MB is opened and the system emits fluorescence. Simultaneously, the DNA-RNA formed by the targeted MicroRNA and MB activates the <i>trans</i>-cleavage activity of LbCas12a, partially cleaving the single-stranded DNA extended from the MB and further enhancing the fluorescence intensity of the system. We designed the MCM-CRISPR/Cas12a system for miRNA-21, miRNA-155, and miRNA-10b and successfully applied it for sensitive and specific imaging of these MicroRNAs both inside and outside cells. This study provides a new idea for the sensitive and specific imaging of multiple MicroRNAs within cells, which is important for studying the distribution and dynamic changes of MicroRNAs in cells.