Ag nanoclusters on ZnO nanodome array as hybrid SERS-active substrate for trace detection of malachite green

•Ag nanoclusters (NCs) were distributed on the relatively flat surfaces of focused ion beam fabricated ZnO nanodome (ND).•The effect of surface enhanced Raman scattering property of Ag NCs on ZnO ND was correlated with the coupling density of NCs upon NDs.•Ag NCs on ZnO ND is attributed to the generation of strong local electromagnetic fields induced by NCs on NDs and intra-NC interactions.•The hybrid Ag NCs on ZnO ND can detect malachite green over a wide range of concentrations at single molecule level. Ag nanoclusters (NCs) were deposited on a focused ion beam (FIB)-fabricated ZnO nanodome (ND) to create a hybrid metal–semiconductor nanosystem for sensing extremely low concentrations of target species. The Ag NCs were uniformly distributed on the top and side surfaces of the ZnO ND. The surface-enhanced Raman scattering (SERS) effect of Ag NCs on ZnO ND was correlated with the coupling density of Ag NCs upon ZnO NDs with an optimized enhancement factor of 106. The improved SERS effect is attributed to the generation of strong local electromagnetic fields induced by the NCs on NDs and intra-NC interactions. In addition, the hybrid nanosystem was found to distinguish malachite green with good reproducibility over a wide range of concentrations down to the single-molecule detection limit (i.e., 10−17M). This unique metal–semiconductor hybrid nanosystem is advantageous for the formation of Raman signal polarization among the excitation laser, nanostructure, and target species with high sensitivity and selectivity and is thus suitable for the trace detection of various target species.