SIMPLE-CRISPR: A Sample-to-Result Platform for Point-of-Care Detection of Nucleic Acids via a Functionalized Magnetic-Bead-Based CRISPR Assay

Clustered regularly interspaced short palindromic repeat (CRISPR) systems show great promise for next-generation molecular diagnostics due to their programmability and specificity. Amplification-free CRISPR detection has a strong potential for point-of-care (POC) testing, and the digital format of the assay naturally improves the sensitivity of amplification-free CRISPR detection. However, integrating sample preparation, reaction implementation, and signal readout into a streamlined and user-friendly POC workflow remains a major technical challenge. We address this by developing SIMPLE-CRISPR (Sample-to-Result Integrated platform with Magnetic-bead extraction, Polydisperse droplets, Low-complexity operation, and Engineered smartphone readout), an amplification-free CRISPR-Cas12a system for POC diagnostics. Our innovation features functionalized magnetic-bead extraction for the efficient enrichment of low-abundance nucleic acid targets from large-volume samples with minimal loss, vortex-driven polydisperse emulsification for facile digital droplet generation, and smartphone-integrated fluorescence imaging for on-site portable signal detection. This integrated approach significantly improves sensitivity compared to bulk CRISPR, removes the need for amplification and complex microfluidics, and provides sample-to-result functionality for POC environments. Clinical validation for human papillomavirus type 18 (HPV18) detection confirmed that the assay achieved diagnostic performance consistent with quantitative real-time polymerase chain reaction (qRT-PCR), demonstrating its great potential for accessible POC nucleic acid diagnostics.