Base-mismatched crRNA in CRISPR Enabled Universal One-pot Rapid Nucleic Acid Detection

Authors

Xu, J., Wang, X., Yuan, B., Hu, M., Xin, W., Wang, J., Ren, H., Yuan, Y.

Abstract

CRISPR-Cas12a-based diagnostics are promising for field detection yet are often constrained by two step workflows or laborious optimization of one-pot reactions. Herein, we present a universal one-pot RPA/CRISPR-Cas12a strategy using base-mismatched crRNA in the seed region (positions 1-6). Introducing of single-nucleotide mismatches (complementary or error) into crRNA suppresses cis-cleavage activity, enabling amplification and detection in a single tube without PAM re-design or costly modified crRNA. Molecular dynamics (MD) simulations indicated that moderate potential energy (PE) variation correlates with improved screening performance, providing guidance for the selection of effective mismatches. This strategy successfully converted established two-step assays for Burkholderia pseudomallei and Brucella into one-pot formats, achieving detection of targets at 10 copies/L within 30 min with good specificity. Lyophilized pellets supported field testing on lithium-ion battery-powered devices, and experiments with simulated soil samples confirm the robustness of the approach. Together, this cost-effective, adaptable strategy can streamline RPA-CRISPR diagnostics for infectious disease surveillance.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 02 Oct 2026.

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