CRISPR/Cas13a: Compensatory Target Activation Mechanism.

Abstract

CRISPR/Cas13a is a powerful RNA-targeting platform for molecular diagnostics, but conventional single-effector systems typically require contiguous RNA targets longer than ∼20-28 nt, limiting sensitivity and target flexibility. CRISPR/Cas13a-CTAM is presented as a compensatory target activation mechanism that facilitates synergistic Cas13a activation through two independently programmable short RNA effectors. By functionally decoupling allosteric activation and binding stabilization, CRISPR/Cas13a-CTAM supports robust activation by ultra-short RNA targets as short as 13 nt, substantially expanding the detectable target range. Compared with traditional single-effector Cas13a assays, CRISPR/Cas13a-CTAM achieves a detection limit of 1 fM for a 13-nt RNA target, representing an approximately tenfold sensitivity improvement. Notably, a single-nucleotide mismatch within the 13-nt target induces up to a 35-fold reduction in apparent cleavage rate, corresponding to a sevenfold enhancement in mismatch discrimination. The dual-effector architecture further enables simultaneous dual-target detection, demonstrated by dual miRNA profiling related to COVID-19 and combined detection of exosome membrane proteins. Moreover, the weakly activating effector was utilized as an anchoring module to achieve the first functional immobilization of Cas13a on a sensing surface, enabling in situ electrochemical miRNA detection. By overcoming the reliance on long RNA targets, CRISPR/Cas13a-CTAM provides a sensitive, programmable platform for RNA diagnostics and integrated biosensor development.