Magnetic nanoparticles with specific surface features are interesting materials for biomedical applications. The combination of molecular interactions on small particles with macroscopic cohesion forces offers unique opportunities. This work reports the synthesis of magnetic core–shell nanoparticles with alkylimidazolium coated surface for effective DNA extraction. A magnetic Fe₂O₃ core was coated with a silica shell and functionalized with an organic halide. This enabled a surface coating with organic cations to mediate effective molecular interactions with polyanionic DNA. The large surface area of the ∼20 nm small particles with a magnetization of 25 emu g⁻¹ enabled high DNA particle loading of 1/30 m% with easy isolation based on an external magnetic field. Moreover, the coating of the particles stabilized DNA against ultrasound initiated fragmentation.