The assembly of nanoframe dimers assisted by aptamer-functionalized smaller spherical gold nanoparticles as prospective surface-enhanced Raman scattering (SERS) biotraps for riboflavin, an important molecule for biological electron transfer reactions, is reported. In this approach, the aptamer-coated gold nanoparticles designed for selective binding of riboflavin also serve as the electrostatic driver for nanoframe dimerization in dilute solutions. The gold nanoframe dimers provide unique conditions for plasmonic coupling in a hot spot with sufficient space for the binding of bulky biomolecules. The use of an aptamer allows for highly selective binding of the targeted analyte as compared with conventional organic ligands with excellent low detection limit of one micromole of riboflavin.