A CRISPR/Cas12a-SERS platform for amplification-free detection of African swine fever virus genes

A surface-enhanced Raman scattering (SERS) strategy combined with a CRISPR/Cas12a system is designed for the amplification-free gene detection of African swine fever virus (ASFV). A SERS sensing probe was fabricated by conjugating plasmonic SERS tags on the magnetic bead (MB) surface with an single-stranded DNA (ssDNA) as a linker. The target ASFV gene-activated Cas12a protein starts the trans-cleavage function on the linker ssDNA, which causes the release of SERS tags, leading to a decrease of the SERS signal detected above the collective MBs. Two signal enhancement strategies were adopted to improve the liquid-phase detection sensitivity arriving at the fM level. One is the unlimited trans-cleavage function of the Cas12a protein, and the other is the magnetic-induced collection of probes that can significantly gather the analytes from the solution to the laser spot and provide SERS hotspots during SERS measurement. Detection range is from 100 nM to 10 fM without the gene amplification steps. This sensing method achieved the SERS detection of ASFV gene in the serum system and the extracted nucleic acids in viral samples with high sensitivity and selectivity at a relative standard deviation of <8%. This sensing platform is mainly in use for site inspection and quick testing of gene samples.