biostudies-literatureShinoda HMEXT | Japan Society for the Promotion of ScienceMEXT | Japan Science and Technology Agency (JST)MEXT | Japan Society for the Promotion of Science (JSPS)Japan Agency for Medical Research and DevelopmentMEXT | Japan Science and Technology AgencyJapan Agency for Medical Research and Development (AMED)476https://www.ebi.ac.uk/biostudies/studies/S-EPMC8055673biostudies-literatureUnknown4(1)CRISPR-based nucleic-acid detection is an emerging technology for molecular diagnostics. However, these methods generally require several hours and could cause amplification errors, due to the pre-amplification of target nucleic acids to enhance the detection sensitivity. Here, we developed a platform that allows "CRISPR-based amplification-free digital RNA detection (SATORI)", by combining CRISPR-Cas13-based RNA detection and microchamber-array technologies. SATORI detected single-stranded RNA targets with maximal sensitivity of ~10 fM in <5 min, with high specificity. Furthermore, the simultaneous use of multiple different guide RNAs enhanced the sensitivity, thereby enabling the detection of the SARS-CoV-2 N-gene RNA at ~5 fM levels. Therefore, we hope SATORI will serve as a powerful class of accurate and rapid diagnostics.Communications biologyAmplification-free RNA detection with CRISPR-Cas13.PMC8055673JPMJCR19H520H0593120he0622032h0001Shinoda HNakagawa RTakahashi CAndo JOkazaki SNakano MTaguchi YNishimasu HNoda TNureki OMakino AWatanabe RMuramoto YTakahashi IfalseAmplification-free RNA detection with CRISPR-Cas13.CRISPR-based nucleic-acid detection is an emerging technology for molecular diagnostics. However, these methods generally require several hours and could cause amplification errors, due to the pre-amplification of target nucleic acids to enhance the detection sensitivity. Here, we developed a platform that allows "CRISPR-based amplification-free digital RNA detection (SATORI)", by combining CRISPR-Cas13-based RNA detection and microchamber-array technologies. SATORI detected single-stranded RNA targets with maximal sensitivity of ~10 fM in <5 min, with high specificity. Furthermore, the simultaneous use of multiple different guide RNAs enhanced the sensitivity, thereby enabling the detection of the SARS-CoV-2 N-gene RNA at ~5 fM levels. Therefore, we hope SATORI will serve as a powerful class of accurate and rapid diagnostics.2021-01-01T00:00:00Z2021 Apr2025-04-05T10:14:44.706Z2025-04-05T10:14:44.706ZS-EPMC80556733387580310.1038/s42003-021-02001-8