A general onepot-method for nucleic acid detection with CRISPR-Cas12a

Abstract CRISPR/Cas12a system has been shown promising for nucleic acid diagnostics due to its rapid, portable and accurate features. In combination with isothermal amplification technology, single-copy sensitivity can be achieved. However, cleavage of the amplicons and primers by the cis- and trans-activity of Cas12a hinders the attempts to integrate the amplification and detection steps into a single reaction. Through phosphorothioate modification of primer and design of crRNA that allow for the cutting site locating at the modified site of the primer, we realized onepot detection of SARS-CoV-2 with single-copy sensitivity. We also identified the activated Cas12a has a much higher affinity to C nucleotide-rich reporter than others. By applying such reporters, we significantly reduced the reaction time required for the lateral-flow readout. Furthermore, to improve the specificity of the strip-based assay, we created a novel reporter and, when combined with a customized strip, the unspecific signal could be completely eliminated. This established system termed Targeting DNA by Cas12a-based Eye Sight Testing in Onepot Reaction (TESTOR) was validated using clinical cervical samples for human papillomaviruses (HPVs) detection. Our system represents a general approach to integrating the nucleic acid amplification and detection into a onepot reaction in CRISPR-Cas systems, highlighting its potential as a rapid, portable and accurate detection platform of nucleic acids.