So far, CRISPR–Cas systems have been repurposed for a variety of applications, including the targeted editing of genomes 15, epigenomes 16 and transcriptomes 17, the bioimaging of nucleic acids 18, the recording of cellular events 19 and the detection of nucleic acids. The crRNA can be programmed towards a specific DNA or RNA region of interest through hybridization to a complementary sequence, which in some systems is restricted to the proximity of a protospacer adjacent motif (PAM) or protospacer flanking sequence 14. Although there are diverse CRISPR–Cas systems among the different species of archaea and bacteria 13, these systems are connected by their dependence on CRISPR RNA (crRNA), which guides Cas proteins to recognize and cleave nucleic acid targets. CRISPR systems are a fundamental part of a microbial adaptive immune system 12 that recognizes foreign nucleic acids on the basis of their sequence to subsequently eliminate them by means of endonuclease activity associated with the CRISPR-associated (Cas) enzyme. Ideally, such next-generation diagnostics should also have single-nucleotide specificity, which is integral to the detection of mutations conferring resistance against antibiotics 10 or antiviral drugs 11.Ĭlustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostics have the potential to fulfil these unmet needs. However, there is a need for technologies that combine the ease of use and cost efficiency of isothermal amplification with the diagnostic accuracy of PCR. The specificity can be improved through additional readouts, in particular by fluorescent probes 7, oligo strand-displacement probes 8 or molecular beacons 9. Although isothermal nucleic acid amplification circumvents the need for thermal cyclers, non-specific amplification can result in lower detection specificity 6. However, the costs of reagents for PCR are high, and the technique requires sophisticated laboratory equipment and trained personnel 5. In fact, PCR is the gold-standard technique for most nucleic-acid-based diagnostics. The versatility, robustness and sensitivity of PCR have made this technology the most commonly used for the detection of DNA and RNA biomarkers. Nucleic acid-based diagnostics relying on the quantitative polymerase chain reaction (qPCR) or on sequencing have been widely adopted, and are frequently used in clinical laboratories. The detection of nucleic acid biomarkers is also critical for agriculture and food safety, for environmental monitoring and in the sensing of biological warfare agents.

During infectious-disease outbreaks, as most recently experienced with the coronavirus disease 2019 (COVID-19) pandemic, fast and precise nucleic-acid-based testing is vital for effective disease control 3, 4. In fact, nucleic-acid-based diagnostics have become the gold standard for various acute and chronic conditions, especially those caused by infectious diseases 2. Nucleic-acid-based biomarkers associated with disease are essential for diagnostics because DNA and RNA can be amplified from trace amounts, which enables their highly specific detection via the pairing of complementary nucleotides. The fast and accurate diagnosis of a disease is central to effective treatment and to the prevention of long-term sequelae 1.

Ease diagnostics