Re-Engineering CRISPR-Cas12a into a Multimodal Biosensing Platform with Programmable Precursor crRNA

The CRISPR-Cas12a system has emerged as a powerful tool for molecular diagnostics due to its trans-cleavage activity. However, its utility in point-of-care testing is constrained by several inherent limitations: strict dependence on DNA for activation, compromised specificity against single-stranded DNA targets, and a basal catalytic rate often insufficient for direct detection. Here, we engineered a class of programmable precursor CRISPR RNAs (pcRNAs), which re-engineer Cas12a into a multimodal biosensing platform. Our platform enables Cas12a to respond to diverse programmable inputs, including direct RNA detection without reverse transcription, and features a built-in autocatalytic circuit for signal amplification. It demonstrates programmable high specificity, discriminating single-nucleotide variants in DNA with selectivity up to 908.7, and achieves high sensitivity by directly detecting synthetic circHER2 RNA, with a detection limit of 0.5 aM. The robust performance of the platform is validated through the quantitative assessment of circHER2 levels in breast cancer cell lines within complex cellular lysates. By employing a modular nucleic acid design strategy, this work breaks the intrinsic functional constraints of Cas12a and establishes a generalizable framework for the development of next-generation intelligent and programmable molecular diagnostic and sensing systems.