Competitive kinetic mechanisms in one-pot isothermal amplification-CRISPR systems: From model construction to performance evaluation

The urgent demand for integrating real-time molecular diagnosis with isothermal amplification and CRISPR-based detection has underscored the critical need for streamlined, single-tube one-pot methodologies. However, such integration is often hindered by temporal incompatibilities, including premature activation of early amplification products by CRISPR components, which leads to primer degradation and reduced amplification efficiency. To address this challenge, we established a dedicated quantitative competitive kinetic framework for enzyme-free isothermal amplification-CRISPR one-pot systems, using hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) as representative models. Two core inhibitory mechanisms were identified: “pre-activation-degradation inhibition”, in which early CRISPR activation degrades amplification intermediates, and “substrate competition inhibition” in which hairpin probes compete with reporter probes for CRISPR trans -cleavage. Corresponding kinetic equations were derived to describe these interactions quantitatively. Systematic experimental validation of key parameters such as DNA activator concentration, reporter probe concentration, hairpin probe concentration, and ribonucleoprotein (RNP) complex concentration, confirmed the reliability and predictive accuracy of the proposed models. These results provide mechanistic insights into the factors governing one-pot HCR/CHA-CRISPR coupling and identify conditions that optimize assay performance. Overall, this study offers a theoretical foundation and experimental guidance for probe design, reaction condition optimization, and sensitivity enhancement in enzyme-free isothermal amplification-CRISPR one-pot platforms, and provides a general reference for the rational integration of isothermal amplification and CRISPR-based detection.