A De Novo Luciferase Bioconjugate for the Cas13-Based Detection of Influenza A

Rapid, accurate, and accessible diagnostics for pathogenic infections are of vital importance for the prevention of disease transmission and mitigation of future pandemics. Biosensors employing the CRISPR nuclease Cas13 have enabled robust detection of viral RNA. However, existing Cas13-based diagnostics primarily utilize fluorescent or lateral flow assay (LFA) readouts, impeding detection in complex sample media. Here, we have developed a luciferase-based Cas13 diagnostic containing a protein-nucleic acid conjugate, coined Selective One-pot LUminescent Nucleic Acid Reporter (SOLUNAR). SOLUNAR utilizes RNA which has been site-selectively bioconjugated to block the binding of a de novo heterodimeric protein pair. In the presence of a viral target, the sensor RNA is cleaved by the collateral activity of Cas13, restoring binding and yielding a luminescent signal by the reconstitution of a tagged de novo split luciferase. An integral component of SOLUNAR, the use of de novo proteins enabled precise engineering of site-selective chemical handles and tunable binding affinities to modulate activity. SOLUNAR selectively detects Influenza A H1N1 at room temperature in one-pot with a limit of detection (LOD) of 1.5 nM without amplification and is compatible with samples containing ≤10% serum. Our findings demonstrate the utility of luminescence in Cas13 diagnostics and reveal the potential applications of this platform to activity-based enzymatic sensing.