Iron (II,III) oxide Fe3O4 nanoparticles (25 and 50 nm NPs) are grafted with amine groups through silanization in order to generate a positively charged coating for binding negatively charged species including DNA molecules. The spatial nature of the coating changes from a 2-D-functionalized surface (monoamines) through a layer of amine oligomers (diethylenetriamine or DETA, about 1 nm in length) to a 3-D layer of polyamine (polyethyleneimine or PEI, thickness ≥ 3.5 nm). These Fe3O4–PEI NPs were prepared by binding short-chain PEI polymers to the iodopropyl groups grafted on the NP surface. In this work, the surface charge density, or zeta potential, of the nanoparticles is found not to be the only factor influencing the DNA binding capacity, which also seems not to be affected by their buffering capacity profile in the range of pH 4–10. This study also allows the investigation of this 3-D effect on the surface of a nanoparticle as opposed to conventional 2-D amine functionalization. The flexibility of the PEI coating, which consists of only 1, 2, and 3° amines, on the nanoparticle surface has a significant influence on the overall DNA binding capacity and the binding efficiency (or N/P ratio). These polyamine-functionalized nanoparticles can be used in the purification of biomolecules and the delivery of drugs and large biomolecules.