Abstract We review the design and synthesis of functionalized nanoparticles for the application in nanobiotechnology. Initially, the modification of the superparamagnetic iron oxide (SPIO) for contrast agents is described. The series of biomolecule-responsive contrast agents are introduced. Next, silica nanoparticle-based probes in 19F NMR are explained. By employing the silica nanoparticles as a signal quencher for NMR signals, the quantitative analysis of the enzymatic activities was accomplished. The design concepts and the results are explained. We also mention the regulation of the cluster formation of gold nanoparticles. Significant changes in optical properties before and after the assembly are presented. Finally, the typical synthetic procedures are also described in the latter part.