Surface Chemistry-Driven Surface-Enhanced Raman Scattering Fingerprinting of Aptamers on Silver Colloids

The surface-enhanced Raman scattering (SERS) spectra of nucleic acids (NAs) often vary substantially across plasmonic substrates. However, systematic comparative studies across the most commonly employed plasmonic platforms remain limited, particularly for structurally complex NAs, such as aptamers. Herein, we investigate the direct SERS fingerprinting of a thiolated aptamer across three representative silver colloidal systems widely used in nucleic-acid SERS studies: intrinsically cationic spermine-modified nanoparticles, post-synthetically spermine-modified citrate colloids, and chloride-modified citrate colloids. The results show that, under the investigated conditions, the surface chemistry appears to primarily determine the dominant adsorption regime, modulating the balance between the backbone electrostatics and nucleobase-metal interactions. Intrinsically cationic nanoparticles preserve folding-dependent spectral differences, whereas negatively charged systems exhibit pronounced coverage-dependent spectral variability, highlighting the sensitivity of the interfacial SERS response to surface coverage and preparation history. These findings highlight that the SERS fingerprint of the aptamer in colloidal suspension largely emerges from the interplay between the structural complexity of the NA and the adsorption regime imposed by the nanoparticle surface chemistry. Therefore, different colloidal substrates can provide complementary spectroscopic information.