Amplification-free detection method for pathogen nucleic acid based on manganese ion enhanced CRISPR system and magnetic enrichment

In this work, we constructed a manganese ion enhanced CRISPR fluorescence analysis platform based on magnetic separation technology and CRISPR/Cas12a system for the amplification-free detection of SARS-CoV-2 RNA. Firstly, nucleic acid functionalized magnetic beads and dual-function signal probes were used to identify conserved sequences of target RNA at the same time, and then the target was captured and separated by magnetic enrichment. The dual-function signal probe is used to bridge the recognition of the target and the output of the fluorescence signal. And the CRISPR activation sequence on the signal probe is used to initiate the downstream CRISPR/Cas12a fluorescence system to generate fluorescent signals. In this method, we used manganese ions to replace the traditional magnesium ions to assist the CRISPR/Cas12a system, which significantly enhanced the analysis effect. Moreover, we designed a variety of signal probes for different regions of the target RNA to further improve the signal intensity. This method can accurately detect the target RNA within 45 minutes, and can effectively identify the positive cases of COVID-19 infection in clinical throat swab samples, which has great potential for clinical application.