Synthetic Protein-to-DNA Input Exchange for Protease Activity Detection Using CRISPR-Cas12a

Anal Chem. 2024 Nov 26;96(47):18645-18654. doi: 10.1021/acs.analchem.4c02622. Epub 2024 Nov 14.

Abstract

We present a novel activity-based detection strategy for matrix metalloproteinase 2 (MMP2), a critical cancer protease biomarker, leveraging a mechanism responsive to the proteolytic activity of MMP2 and its integration with CRISPR-Cas12a-assisted signal amplification. We designed a chemical translator comprising two functional units─a peptide and a peptide nucleic acid (PNA), fused together. The peptide presents the substrate of MMP2, while the PNA serves as a nucleic acid output for subsequent processing. This chemical translator was immobilized on micrometer magnetic beads as a physical support for an activity-based assay. We incorporated into our design a single-stranded DNA partially hybridized with the PNA sequence and bearing a region complementary to the RNA guide of CRISPR-Cas12a. The target-induced nuclease activity of Cas12a results in the degradation of FRET-labeled DNA reporters and amplified fluorescence signal, enabling the detection of MMP2 in the low picomolar range, showing a limit of detection of 72 pg/mL. This study provides new design principles for a broader applicability of CRISPR-Cas-based biosensing.

MeSH terms

  • Biosensing Techniques / methods
  • CRISPR-Associated Proteins / chemistry
  • CRISPR-Associated Proteins / metabolism
  • CRISPR-Cas Systems* / genetics
  • DNA / chemistry
  • DNA / metabolism
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / metabolism
  • Fluorescence Resonance Energy Transfer
  • Humans
  • Matrix Metalloproteinase 2* / genetics
  • Matrix Metalloproteinase 2* / metabolism
  • Peptide Nucleic Acids / chemistry
  • Peptide Nucleic Acids / metabolism
  • Peptides / chemistry
  • Peptides / metabolism

Substances

  • Matrix Metalloproteinase 2
  • DNA
  • Peptide Nucleic Acids
  • CRISPR-Associated Proteins
  • Peptides
  • DNA, Single-Stranded
  • MMP2 protein, human