We present a systematic study on the preparation, characteration and potential application of Fe3O4 and Fe3O4@SiO2 nanoparticles. Fe3O4 nanoparticles of controllable diameters were successfully synthesized by solvothermal system with tuning pH. The magnetic properties of nanoparticles were measured by vibration sample magnetometer. Fe3O4@ SiO2 nanoparticles were obtained via classic Stöber process. Streptavidin coated Fe3O4@SiO2 nanoparticles were prepared by covalent interaction. The quantity of streptavidin bound to nanoparticles was determined by UV-Vis spectrometer. To evaluate the binding efficiency and capacity of nucleic acid on nanoparticles, the capture of biotinylated oligonucleotide on streptavidin coated Fe3O4@SiO2 nanoparticles at different concentration was estimated by fluorescence detection. Both Fe3O4 and Fe3O4@SiO2 nanoparticles exhibited well crystallization and magnetic properties. The maximal amount of streptavidin immobilized onto the Fe3O4@SiO2 nanoparticles was 29.3 microg/mg. The saturation ratio of biotinylated oligonucleotides captured on streptavidin coated Fe3O4@SiO2 nanoparticles was 5 microM/mg within 20 minutes, indicating that FeO4@SiO2 nanoparticles immobilized by streptavidin were excellent carriers in nucleic acid analysis due to their convenient magnetic-separation property. Therefore, the synthesized Fe3O4 and Fe3O4@SiO2 nanoparticles with controllable size and high magnetic saturation have shown great application potentials in nucleic acid research.