Rigidity-Responsive Fluorescence Polarization Detection of Aflatoxin B ₁ via Programmable RCA-Coupled CRISPR/Cas12a and a Conformation-Restricted Depolarization Reporter

Aflatoxin B₁ (AFB₁) is one of the most toxic and carcinogenic mycotoxins, and its trace-level determination in complex food matrices remains a major analytical challenge. Conventional chromatographic methods, while highly accurate, rely on expensive instrumentation and labor-intensive sample pretreatment, whereas most CRISPR/Cas-based biosensors depend on fluorescence intensity turn-on readouts that are vulnerable to matrix autofluorescence, photobleaching, and signal instability, limiting their reliability in real samples. Herein, we propose a rigidity-responsive fluorescence polarization (FP) biosensing strategy that integrates aptamer-based molecular recognition, rolling circle amplification (RCA), and CRISPR/Cas12a trans-cleavage for robust and matrix-tolerant AFB₁ detection. In this system, target binding induces the release of a complementary DNA strand from an immobilized aptamer duplex, initiating padlock probe circularization and RCA to generate abundant Cas12a-activating amplicons. A rationally engineered conformation-restricted depolarization reporter (CRD-Reporter), in which the fluorophore is confined within a rigid duplex framework, provides an intrinsically high FP signal. Upon Cas12a activation, collateral cleavage disrupts the rigid architecture, releasing freely rotating fragments and producing a pronounced FP decrease. Unlike intensity-based CRISPR assays, the FP readout effectively suppresses background interference and signal fluctuations. The proposed assay exhibits a wide linear range from 0.003 to 300 ng/mL with a low detection limit of 0.00113 ng/mL, high specificity, and excellent accuracy in grains, peanuts, and tea samples. This work establishes a robust FP-based CRISPR sensing paradigm for reliable mycotoxin monitoring in complex food systems.