Integrated CRISPR-Cas12a-Based Biosensors with Subwavelength Grating Microring Resonators for Ultrasensitive Mutation-Specific Detection.

The rapid and precise detection of nucleic acids is critical for identifying viral mutations, yet it presents formidable difficulties for conventional diagnostics. While established techniques such as quantitative polymerase chain reaction and next-generation sequencing involve complex workflows, emerging on-chip integrated photonic biosensing techniques are often limited by inadequate specificity and sensitivity. Here, we introduce an integrated photonic biosensing platform that synergizes the programmable recognition of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas12a, with the superior sensitivity of subwavelength grating microring resonators. The sensor surface is functionalized with single-stranded DNA probes conjugated to gold nanoparticles. Upon target recognition, activated Cas12a cleaves the probes, releasing the nanoparticles and generating a quantifiable resonance wavelength shift. In particular, the spectral response gets further amplified by a resonance-enhanced photothermal effect. The detection of SARS-CoV-2 variants enables discrimination between wild-type, Delta, and Omicron strains. The extracted detection limit of 0.7 fM represents a four-order-of-magnitude improvement over conventional fluorescence-based CRISPR assays. Our work establishes a generalizable platform for ultrasensitive, mutation-resolved molecular diagnostics on a CMOS-compatible photonic chip, paving the way for advanced point-of-care testing and genomic surveillance.