Universal and Naked-Eye Gene Detection Platform Based on the Clustered Regularly Interspaced Short Palindromic Repeats/Cas12a/13a System

• Published in: Analytical chemistry (Washington) Vol. 92; no. 5; pp. 4029 - 4037
• Main Authors: Yuan, Chaoqun, Tian, Tian, Sun, Jian, Hu, Menglu, Wang, Xusheng, Xiong, Erhu, Cheng, Meng, Bao, Yijuan, Lin, Wei, Jiang, Jieming, Yang, Chengwei, Chen, Qian, Zhang, Huang, Wang, Heng, Wang, Xiran, Deng, Xianbo, Liao, Xiaoping, Liu, Yahong, Wang, Zhang, Zhang, Guihong, Zhou, Xiaoming
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 03.03.2020
• Subjects: African swine fever; African Swine Fever Virus - genetics; Aggregation behavior; Analytical chemistry; Animals; Asfarviridae; Bacteria - genetics; Chemistry; Cleavage; Colorimetry; Colorimetry - methods; CRISPR; CRISPR-Cas Systems - genetics; Deoxyribonucleic acid; DNA; DNA probes; DNA Probes - chemistry; DNA, Viral - analysis; DNA, Viral - chemistry; Genomic analysis; Gold - chemistry; Livestock; Metal Nanoparticles - chemistry; MicroRNAs - analysis; MicroRNAs - chemistry; Nanoparticles; Promoter Regions, Genetic; RNA, Ribosomal, 16S - analysis; RNA, Ribosomal, 16S - chemistry; rRNA 16S; Swine; Viruses
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/acs.analchem.9b05597

Gold-nanoparticles-based colorimetric assay is an attractive detection format, but is limited by the tedious and ineffective posthybridization manipulations for genomic analysis. Here, we present a new design for a colorimetric gene-sensing platform based on the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system. In this strategy, programmable recognition of DNA by Cas12a/crRNA and RNA by Cas13a/crRNA with a complementary target activates the trans-ssDNA or -ssRNA cleavage. Target-induced trans-ssDNA or ssRNA cleavage triggers an aggregation behavior change for the designed AuNPs–DNA probes pair, enabling the completion of naked-eye gene detection (transgenic rice, African swine fever virus, and miRNAs as the models) within 1 h. This platform is also showing promise as a fast and inexpensive tool for bacteria identification using 16S rDNA or 16S rRNA. A CRISPR/Cas-based colorimetric platform shows superior characteristics, such as probe universality, compatibility with isothermal reaction conditions, on-site detection capability, and high sensitivity, thus, demonstrating its use as a robust next-generation gene detection platform.