Surface-enhanced Raman scattering (SERS) spectroscopy plays an important role in enabling high-precision detection and non-invasive diagnostics. Periodic metallic nanostructures with strong electromagnetic fields and tunable localized surface plasmon resonance can achieve high SERS sensitivity, but fabricating such nanostructures remains a challenge. In this work, the anodic aluminum oxide (AAO) nanocavity template-assisted process of fabricating periodic nanostructures with modulating morphologies from Ag nanoclaws (AgNCWs) to Ag nanocones (AgNCEs) is proposed. The morphologies-related SERS performances of nanostructures are analyzed by using rhodamine 6 g (R6G) as a probe molecule and the optimized AgNCEs possess a limit of detection (LOD) of 1 × 10−9 M. A sandwich strategy is applied to detect SARS-CoV-2 S protein in phosphate-buffered saline (PBS) and pharyngeal swab solution (PSS). The ACE2-modified AgNCEs (ACE2/AgNCEs) structure is applied to bind to the SARS-CoV-2 S protein. The 4-MBA and SARS-CoV-2 S antibody functionalized Au nanoparticles (AuNPs) are used as nanotags. By forming the ACE2/AgNCEs-SARS-CoV-2 S protein-nanotags sandwich structure, characteristic peak intensities of 1580 cm−1 are used as the report signal, and the LOD for SARS-CoV-2 S protein in PBS and PSS solution are 10 fg/mL.
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