BackgroundPolymer surface-modified inorganic nanoparticles (NPs) provide a multifunctional platform for assisting gene delivery. Rational structure design for enhancing colloidal stability and cellular uptake is an important strategy in the development of safe and highly efficient gene vectors.ResultsHeterogeneous Au-coated Fe3O4 (Fe3O4@Au) NPs capped by polyethylene glycol-b-poly1-(3-aminopropyl)-3-(2-methacryloyloxy propylimidazolium bromine) (PEG-b-PAMPImB-Fe3O4@Au) were prepared for DNA loading and magnetofection assays. The Au outer shell of the NPs is an effective platform for maintaining the superparamagnetism of Fe3O4 and for PEG-b-PAMPImB binding via Au–S covalent bonds. By forming an electrostatic complex with DNA at the inner PAMPImB shell, the magnetic nanoplexes offer steric protection from the outer corona PEG, thereby promoting high colloidal stability. Transfection efficiency assays in human esophageal cancer cells (EC109) show that the nanoplexes have high transfection efficiency at a short incubation time in the presence of an external magnetic field, due to increased cellular internalization via magnetic acceleration. Finally, after transfection with the magnetic nanoplexes EC109 cells acquire magnetic properties, thus allowing for selective separation of transfected cells.ConclusionPrecisely engineered architectures based on neutral-cationic block copolymer-conjugated heterogeneous NPs provide a valuable strategy for improving the applicability and efficacy of synthesized vectors.Electronic supplementary materialThe online version of this article (doi:10.1186/s12951-017-0290-5) contains supplementary material, which is available to authorized users.