The ability to harness the nanoscale structural properties is essential for the exploration of functional properties of nanomaterials. This report demonstrates a novel strategy exploring bifunctional nanoparticles for spectroscopic detection and magnetic intervention of DNA assembly, disassembly, and enzyme cutting processes in a solution phase. In contrast to existing single-function based approaches, this strategy exploits magnetic MnZn ferrite nanoparticles decorated with gold or silver on the surface to retain adequate magnetization while producing sufficient plasmonic resonance features to impart surface-enhanced Raman scattering (SERS) functions. The decoration of MnZn ferrite nanoparticles with Au or Ag (MZF/Au or MZF/Ag) was achieved by thermally activated deposition of Au or Ag atoms/nanoparticles on MZF nanoparticles. Upon interparticle double-stranded DNA linkage of the MZF/Au (or MZF/Ag) nanoparticles with gold nanoparticles labeled with a Raman reporter, the resulting interparticle "hot spots" are shown to enable real time SERS monitoring of the DNA assembly, disassembly, or enzyme cutting processes, where the magnetic component provides an effective means for intervention of the biomolecular processes in the solution. The unique bifunctional combination of the SERS "hot spots" and the magnetic separation capability serves as the first example of bifunctional nanoprobes for biomolecular recognition and intervention.