G-triplex: A new type of CRISPR-Cas12a reporter enabling highly sensitive nucleic acid detection

CRISPR-Cas12a (Cpf1) trans-cleaves ssDNA and this feature has been widely harnessed for nucleic acid detection. Herein, we introduce a new type of Cas12a reporter, G-triplex (G3), and a highly sensitive biosensor termed G-CRISPR. We proved that Cas12a trans-cleaves G3 structures in about 10 min and G3 can serve as an excellent reporter based on the cleavage-induced high-order structure disruption. G3 reporter improves the analytical sensitivity up to 20 folds, enabling the detection of unamplified and amplified DNA as low as 50 pmol and 0.1 amol (one copy/reaction), respectively. G-CRISPR has been utilized for the analysis of 27 PCR-amplified patient samples with HPV infection risk based on both fluorescence and lateral flow assays, resulting in 100% concordance between the two. In comparison with the clinical results, it achieved overall specificity and sensitivity of 100% and 94.7%, respectively. These results suggest that G-CRISPR can serve as a rapid, sensitive, and reliable biosensor, and could further expand the CRISPR toolbox in biomedical diagnostics. •CRISPR-Cas12a trans-cleaves G-triplex structures.•G-triplex formed by TBA11 is a promising Cas12a-based biosensing reporter.•TBA11 reporter enhances the detection sensitivity up to 20 folds over normal ssDNA reporter.•The LOD of our assay achieved 0.1 aM for the amplified HPV16 plasmid.•A specificity and sensitivity of 100% and 94.7% was achieved in the detection of HPV patient samples.