Target DNA-Mediated Plasmonic Coupling and Assembly Kinetics of Gold Nanorods for Label-Free Nucleic Acid Detection

DNA-mediated assembly of plasmonic nanoparticles provides a versatile platform for controlling interparticle separation, thereby enabling a systematic investigation of plasmonic coupling and localized electromagnetic hotspot formation. Here, we report the sequence-specific assembly of DNA-functionalized gold nanorods (AuNRs) using a sesame allergen-derived single-stranded DNA (ssDNA) as a molecular bridge. Keeping the concentration of the DNA-functionalized AuNRs constant, the target ssDNA concentration was systematically varied from 0.25 to 500 nM, and the resulting assembly process was monitored by extinction spectroscopy, revealing pronounced target-concentration-dependent plasmonic coupling. Time-dependent extinction measurements and kinetic analysis showed that the apparent assembly rate constant increased monotonically with the target concentration, demonstrating accelerated assembly at higher target availability. Scanning transmission electron microscopy (STEM) confirmed the formation of progressively larger AuNR assemblies with increasing target concentration, consistent with the concentration-dependent optical response. The assembled nanorods also generated plasmonic hotspots that enabled reporter-free surface-enhanced Raman scattering (SERS) detection of the target DNA with a limit of detection of 2 pM, substantially lower than that obtained by the extinction-based assay (1.7 nM). These results establish a direct relationship among target concentration, DNA-mediated assembly, plasmonic coupling, and Raman enhancement, providing mechanistic insight into hybridization-driven plasmonic nanoparticle assembly.