RNA target-independent non-canonical activation (RINCA) of Cas13 trans-nuclease activity

A thorough understanding of unintended Cas13 activity is critical for ensuring the safe in vivo application of CRISPR-Cas13. In this study, we uncover the RNA target-independent, non-canonical activation (RINCA) of Cas13 by crRNA alone and elucidate its structural basis. RINCA poses both challenges and opportunities for Cas13-based technologies. On one hand, it constrains Cas13's utility due to its uncontrolled RNase activity. To address this, we screened over 40 rationally designed Cas13a mutants to identify those with diminished RINCA potential while preserving target-dependent responses. These optimized Cas13a variants improve biosensing sensitivity and significantly reduce cytotoxicity in vivo. On the other hand, RINCA can be harnessed for novel applications. By integrating RNA aptamers into spacer regions, the RINCA-capable LwCas13a/ap-crRNA system was engineered to sense intracellular metabolite levels, drive systemic RNA degradation, and demonstrate anti-cancer efficacy across multiple models. This study not only discovers the RINCA model of Cas13 activity but also provides effective mitigation strategies and establishes novel RINCA-based applications.