Gold-silver core-shell nanodumbbells in solution state as a highly sensitive and reproducible assay platform for bacterial genome detection

Surface-enhanced Raman scattering (SERS) has been investigated as a promising spectroscopic tool for various assay platforms. However, key challenges, such as the reproducibility and sensitivity of this tool should be addressed to enable it to become a reliable and practical method for future clinical applications. Although the single-molecule sensitivity of SERS has already been proven in dry state analysis, its signal reproducibility remains a key challenge in developing a real assay platform. The signal reproducibility of SERS can be significantly improved by obtaining the Raman signal from the solution state; however, the sensitivity of this method is not satisfactory. In this study, we demonstrate a method to overcome both key challenges by using a solution-state formation of gold-silver core-shell nanodumbbells (GSNDs) with target nucleic acid and nanoscale Ag shell formation, which was proven to exhibit single-molecule sensitivity in dry state analysis. To utilize the concept of a reliable assay platform in solution, diverse parameters such as the length of the target sequences, hybridization conditions, number density of probe sequences, and the Ag shell thickness are investigated. The hybridization yield of Au dimer reaches up to 79.36% for E. faecalis, indicating that the hybridization yields are target sequence dependent. It is strongly correlated with detection limit for the target bacteria. The solution-state GSND-based assay shows a highly sensitive results for bacterial target DNA with no mutual interference and excellent reproducibility. The method can identify extremely low concentrations of bacteria (4.5 cfu mL⁻¹), which is much superior to the conventional PCR (4500 cfu mL⁻¹) and culture-based assays (45 cfu mL⁻¹). The results envision the current GSND-based assay as a promising assay platform for future clinical applications.