Programmable Versatile Socket: A Tight-Locking and High-Gain CRISPR/Cas12a Molecular Circuit for Ultrasensitive Sensing of Diverse Targets

Abstract

CRISPR/Cas12a has emerged as an important platform for nucleic acid analysis, yet limited catalytic turnover and intrinsic nucleic acid specificity constrain its sensitivity and analyte scope. Herein, a tight-locking and high-gain Cas12a-driven strand displacement amplification (CSDA) molecular circuit is developed as a versatile socket without preamplification for programmable sensing of nucleic acid and non-nucleic acid analytes. CSDA relies on an RNA–DNA three-strand hairpin (RD-TSH) switch containing a 2-nt mismatch. RD-TSH suppresses nonspecific amplification and unintended Cas12a self-activation to ensure tight locking. Screening the number of mismatched bases in RD-TSH and molecular-level mechanistic analyses reveal a DNA breathing-driven two-step unlocking mechanism. Only complete unlocking triggers autocatalytic CSDA, allowing high-gain amplification. The sequence-independent unlocking of RD-TSH confers high orthogonality to CSDA, enabling target-specific modules to be coupled to the CSDA socket as interchangeable plugs via programmable crRNA guides, thus achieving universal detection of both nucleic and non-nucleic analytes. Using Vibrio parahaemolyticus DNA, thermostable direct hemolysin, and aflatoxin B1 as representative targets, CSDA achieved ultrasensitive detection in complex matrices with sensitivity improvements of over 5 orders of magnitude, 42-fold, and 602-fold, respectively. This plug-and-play architecture establishes CSDA as a broadly adaptable and ultrasensitive CRISPR/Cas12a sensing socket, providing a general route toward programmable sensing of diverse analyte classes and a promising strategy for more accurate integrated multitarget analytical platforms.