Surface-enhanced Raman scattering (SERS)-based signal amplification and detection methods using plasmonic nanostructures have been widely investigated for imaging and sensing applications. However, SERS-based molecule detection strategies have not been practically useful because there is no straightforward method to synthesize and characterize highly sensitive SERS-active nanostructures with sufficiently high yield and efficiency, which results in an extremely low cross-section area in Raman sensing. Here, we report a high-yield synthetic method for SERS-active gold-silver core-shell nanodumbbells, where the gap between two nanoparticles and the Raman-dye position and environment can be engineered on the nanoscale. Atomic-force-microscope-correlated nano-Raman measurements of individual dumbbell structures demonstrate that Raman signals can be repeatedly detected from single-DNA-tethered nanodumbbells. These programmed nanostructure fabrication and single-DNA detection strategies open avenues for the high-yield synthesis of optically active smart nanoparticles and structurally reproducible nanostructure-based single-molecule detection and bioassays.