Spatially blocked split CRISPR-Cas12a system for ultra-sensitive and versatile small molecule activation and detection

Hao Hu, Songcheng Guo, Yiyuan Li, Kejun Dong, Yan Lu, Keyi Ye, Longjie Li (), Xiaoyu Zhou (), Liming Cheng () and Xianjin Xiao ()
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Hao Hu: Huazhong University of Science and Technology
Songcheng Guo: Huazhong University of Science and Technology
Yiyuan Li: Wuhan Polytechnic University
Kejun Dong: Huazhong University of Science and Technology
Yan Lu: Huazhong University of Science and Technology
Keyi Ye: Huazhong University of Science and Technology
Longjie Li: Wuhan Polytechnic University
Xiaoyu Zhou: City University of Hong Kong
Liming Cheng: Huazhong University of Science and Technology
Xianjin Xiao: Huazhong University of Science and Technology

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Detecting small molecules is pivotal across fields like clinical diagnostics, environmental monitoring, and food safety. The CRISPR-Cas12a system, known for its simplicity and sensitivity, offers a promising basis for small molecule detection. However, current CRISPR-based detection methods face challenges, including complex design requirements, high background noise, and limited adaptability to different targets. In our study, we introduce the SBS-Cas system, leveraging a split crRNA mode to induce spatial hindrance on the scaffold strand through molecular binding. This approach prevents the assembly with Cas12a, effectively masking its trans-cleavage activity. By introducing small molecules that competitively bind to the macromolecule, we eliminate this spatial hindrance, activating Cas12a. Our results demonstrate high sensitivity, versatility, and adaptability in small molecule detection across multiple reactions, with successful intracellular imaging and responsive fluctuations in complex environments underscoring the system’s robustness. This innovative CRISPR-Cas12a-based approach establishes a low-background, highly sensitive platform for small molecule detection. SBS-Cas promises not only to enhance tools for clinical, environmental, and food safety applications but also to advance CRISPR research, providing insights and expanding possibilities in molecular detection science.

Date: 2025
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DOI: 10.1038/s41467-025-60265-8

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