The contamination of mycotoxins poses a serious threat to global food security, hence the urgent need for simultaneous detection of multiple mycotoxins. Herein, two SERS nanoprobes were synthesized by embedded SERS tags (4-mercaptopyridine, 4MPy; 4-mercaptobenzonitrile, TBN) into the Au and Ag core–shell structure, and each was coupled with the aptamers specific to ochratoxin A (OTA) and zearalenone (ZEN). Meanwhile, a rigid enhanced substrate Indium tin oxide glass/AuNPs/Graphene oxide (ITO/AuNPs/GO) was combined with aptamer functionalized Au@AgNPs via π-π stacking interactions between the aptamer and GO to construct a surface-enhanced Raman spectroscopy (SERS) aptasensor, thereby inducing a SERS enhancement effect for the effective and swift simultaneous detection of both OTA and ZEN. The presence of OTA and ZEN caused signal probes dissociation, resulting in an inverse correlation between Raman signal intensity (1005 cm−1 and 2227 cm−1) and the concentrations of OTA and ZEN, respectively. The SERS aptasensor exhibited wide linear detection ranges of 0.001–20 ng/mL for OTA and 0.1–100 ng/mL for ZEN, with low detection limits (LOD) of 0.94 pg/mL for OTA and 59 pg/mL for ZEN. Furthermore, the developed SERS aptasensor demonstrated feasible applicability in the detection of OTA and ZEN in maize, showcasing its substantial potential for practical implementation.
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