From Self-Processing to Responsive Assembly Enabling an Autocatalytic Cas13a Circuit for Enhanced Biosensing

Despite the success of non-classical crRNA designs in Cas12a-based biosensing, application to Cas13a systems faces fundamental challenges. Our research discovers that site-specific splitting within the crRNA seed region enables effective activation of Cas13a trans-cleavage. Here, we developed an autocatalytic Cas13a circuit that transitions from self-processing to responsive assembly for enhanced biosensing (PRA-Cas13a). The system employs engineered pre-crRNA as a molecular switch, which undergoes self-processing upon target binding to assemble an active Cas13a complex and activate its trans-cleavage activity. By integrating a dual-UUU site DNA switch template and a T7 RNA polymerase-mediated signal amplification module, a "processing-assembly-amplification" cycle is constructed to enhance the detection signal. Through validation using various targets including miRNA, mRNA, and viral DNA, the PRA-Cas13a system not only achieves an attomolar (aM) level detection limit but also enables visual field detection within 10 min using a lateral flow test strip. Analysis of single-base mutations demonstrated that its sensitivity is significantly superior to conventional CRISPR-based methods. Moreover, the system successfully enabled accurate detection of survivin mRNA in different cell lines and HPV16 in clinical cervical swab samples, showing strong concordance with qPCR gold standard methods. The PRA-Cas13a strategy leverages intrinsic self-processing assembly and autocatalytic signal amplification, addresses the critical issue of off-target cleavage inherent in conventional Cas13a systems while expanding the range of applicable targets, and demonstrates high specificity and point-of-care testing potential in cancer and viral diagnostics.