CRISPR-empowered electrochemical biosensor for target amplification-free and sensitive detection of miRNA

The clustered regularly interspaced short palindromic repeats (CRISPR) system provides a new molecular diagnostic tool for construction of biosensor platforms due to its high programmability and target specificity. Herein, we developed a CRISPR-empowered electrochemical biosensor by combining the advantages of CRISPR/ Cas13a and primer exchange reaction (PER), named PER-E-CRISPR, for target amplification-free and sensitive detection of miR-21. Dual-signal amplification procedures involve the binding of target miR-21 induced by CRISPR-based amplification, along with the hybridization of multiple short single-stranded DNA strands with PER concatemers. When target miR-21 is present, CRISPR/Cas13a specifically recognizes the target miRNA, triggering the trans-cleavage activity of CRISPR/Cas13a. Then Cas13a/crRNA/miRNA cleaved the predesigned ribonucleotide site in hairpin 1 (HP1) and released trigger to open hairpin 2 (HP2) modified on the electrode surface. Then PER bridge sequence contained in HP2 is exposed and hybridized with PER concatemers, following multiple short single-stranded DNA tagged with methylene blue (ssDNA-MB) bond with the PER concatemers. Under optimized conditions, PER-E-CRISPR assay for detecting miR-21 exhibits linearity in dynamic range from 10-13 to 10- 7 M, and we obtained a limit of detection (LOD) of 30.2 fM. The established PER-E-CRISPR biosensor shows perfect practical performance in actual plasma, which may have great promising prospects for miRNA detection in the field of molecular diagnosis.

Automated summary

We developed a CRISPR-empowered electrochemical biosensor, named PER-E-CRISPR, for amplification-free and sensitive detection of miR-21. The biosensor combines the advantages of CRISPR/Cas13a and primer exchange reaction (PER) for target amplification. Under optimized conditions, the PER-E-CRISPR assay exhibits a linear range from 10-13 to 10-7 M and a limit of detection of 30.2 fM. The biosensor shows excellent performance in actual plasma, indicating promising prospects for miRNA detection in molecular diagnosis.