Ultra-sensitive biosensor detection of microRNA based on the CRISPR/Cas12a system and exonuclease-assisted target recycling signal amplification

MicroRNAs (miRNAs) are essential regulators of gene expression and are significantly involved in both preventing and treating a range of diseases. To that end, we developed an ultra-sensitive detection method for miRNA-141 by integrating exonuclease-assisted target recycling signal amplification with the CRISPR/Cas12a system. This method employs a variable hairpin probe (HP) designed to hybridize with miRNA, which, under the action of exonuclease III (ExoIII), cleaves the hairpin probe and triggers target recycling signal amplification. This results in the formation of output DNAs (ODs) containing multiple repeat sequences. The CRISPR/Cas12a system identifies these repeated sequences in ODs through its crRNA component, which in turn triggers the trans-cleavage function of the Cas12a/crRNA complex. It leads to the cleavage of a fluorescently quenched reporter probe. Consequently, this process restores fluorescence, producing a significantly enhanced fluorescent signal that facilitates the detection of miRNA-141, achieving a detection threshold down to 62 fM. This detection approach can specifically differentiate miRNA-141 from other confounding substances and has effectively identified low concentrations of miRNA-141 in actual sample human serum and diverse cancer cell lysates, showcasing its capability for tracing various nucleic acid biomarkers at minimal levels.