Plug-and-Play Photo-Initiated CRISPR–Cas12a One-Pot Nucleic Acid Detection via Universal Repeat RNA Acylation Strategy

Precise spatiotemporal control of CRISPR activity is central to both accurate gene editing and sensitive molecular diagnostics. However, current regulatory strategies are often sequence-specific, labor-intensive, and difficult to generalize. Here, we report a minimalist plug-and-play tactic: acylation of the repeat region (rRNA) of a split crRNA with photolabile groups. Because the modification is introduced post-synthesis and is independent of the spacer region (sRNA), every rRNA, regardless of its target sequence, can be activated by light irradiation alone, entirely eliminating the need for redesign or reoptimization. Integrating the photo-initiated CRISPR-Cas12a system with recombinase polymerase amplification into a one-pot format yields an upgraded platform, named POIROTv2 (PhotO-Initiated CRISPR-Cas12a system for Robust One-pot Testing, version 2). POIROTv2 achieves a 100-fold sensitivity gain over conventional always-on Cas12a-based one-pot assays and matches the analytical performance of a two-step assay while remaining a more streamlined and potentially faster detection process and avoiding the risk of aerosol contamination. In clinical validation with HCMV- and EBV-suspected samples, POIROTv2 delivered diagnostic accuracy statistically indistinguishable from that of gold-standard qPCR, highlighting its potential for robust and sensitive molecular diagnostics. Overall, the strategy opens up exciting possibilities for applications in infectious virus diagnostics and has broad prospects in the field of spatiotemporally controllable gene editing.