Viral nucleic acid detection with CRISPR-Cas12a using high contrast cleavage detection on micro-ring resonator biosensors

Abstract

Micro-ring resonators have emerged as a powerful platform for analyzing and detecting biomolecules at low concentrations. Here we demonstrate a high contrast cleavage detection (HCCD) assay on a micro-ring resonator to sense the cleavage of DNA reporterslinked to high-contrast nanoparticles (NPs), leading to dramatic optical signal amplification. The HCCD mechanism is coupled with a CRISPR-Cas12a assay for rapid and sensitive on-chip nucleic acid detection. Leveraging high-contrast gold nanoparticle (AuNP) reporters, an ~8 nm resonance shift is observed by using a 1 nM of complementary DNA (cDNA) target, matching part of the SARS-CoV-2 sequence. In addition, we show that a micro-ring resonator can not only record the entire surface functionalization process, as has been show previously, but also monitor CRISPR reactions in-situ. This work is the first step toward novel nucleic acid amplification-free detection via a combination of integrated photonics and CRISPR-Cas collateral cleavage assays.