The effect of different functional groups on binding capacity of DNA was studied with bare and modified superparamagnetic iron oxide nanoparticles (SPIONs). For this purpose, modifications were performed with [3-(2,3-epoxypropoxy)propyl] trimethoxy silane (GPTS) and (3-aminopropyl) triethoxysilane (APTS) by silanization reaction and also subsequent reaction with glutaraldehyde (GA) to obtain functional groups on nanoparticles surface. L-myc gene from breast tissue with cancer was amplified by using polymerase chain reaction (PCR). APTS functionalized nanoparticles showed the highest binding capacity (82.70%) when compared with bare, GPTS, APTS and GA functionalized SPIONs. DNA immobilized magnetic nanoparticles were also examined by Scanning Electron Microscopy. Binding capacity of irinotecan to DNA onto SPIONs was found as 2.81×10-5 mg/mL for 20 mg of APTS modified nanoparticles by using fluorescence spectroscopy. © 2013 Elsevier B.V.