The aim of this study is to investigate the applicability of streptavidin carrying magnetic nanoparticles in electrochemical nucleic acid sensor systems. The magnetite (Fe3O4) nanoparticles were prepared by co-precipitation technique, and then they were coated with a carboxylic acid containing polymer layer. Streptavidin molecules were immobilized onto the surfaces of these magnetic nanoparticles (with two different average diameter of 125 and 225 nm) via these functional groups. An electrochemical nucleic acid sensor system composed of a disposable graphite sensor, pencil graphite electrode (PGE) and differential pulse voltammetry (DPV) was used for measurement of guanine oxidation signal observed at + 1.0 V. In the hybridization tests biotinylated inosine substituted probe was immobilized onto the magnetic nanoparticles and hybridization with its complementary target at the surface of particles within the medium was exhibited successfully by using this electrochemical sensor system. For electrochemical detection of sequence specific DNA hybridization and its selectivity studies, the biotinylated hepatitis B Virus (HBV) wild type probe was immobilized onto the nanoparticles. ne guanine oxidation signals were measured in the solutions containing no target, the complementary target, a single-base mismatch target, and noncomplementary target oligonucleotides. A significant guanine oxidation signal (71 nA) was observed with the complementary target due to complete hybridization, while with single-base mismatch target, the signal at the same conditions was quite low about 14 nA. However, in the case of the noncomplementary target, there was a low but observable mean signal about 9 nA (showing the nonspecific interaction). The detection limit (S/N = 3) was found as 43.11 pmol/mL target concentration obtained in 20 min hybridization time.