Highly
sensitive, reliable assays with strong multiplexing capability
for detecting nucleic acid targets are significantly important for
diagnosing various diseases, particularly severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2). The nanomaterial-based assay
platforms suffer from several critical issues such as non-specific
binding and highly false-positive results. In this paper, to overcome
such limitations, we reported sensitive and remarkably reproducible
magnetic microparticles (MMPs) and a surface-enhanced Raman scattering
(SERS)-based assay using stable silver nanoparticle clusters for detecting
viral nucleic acids. The MMP–SERS-based assay exhibited a sensitivity
of 1.0 fM, which is superior to the MMP-fluorescence-based assay.
In addition, in the presence of anisotropic Ag nanostructures (nanostars
and triangular nanoplates), the assay exhibited greatly enhanced sensitivity
(10 aM) and excellent signal reproducibility. This assay platform
intrinsically eliminated the non-specific binding that occurs in the
target detection step, and the controlled formation of stable silver
nanoparticle clusters in solution enabled the remarkable reproducibility
of the results. These findings indicate that this assay can be employed
for future practical bioanalytical applications.