DNA and silica-coated magnetic particles entangle and form visible aggregates under chaotropic conditions with a rotating magnetic field, in a manner that enables quantification of DNA by image analysis. As a means of exploring the mechanism of this DNA quantitation assay, nanoscale SiO₂-coated Fe₃O₄ (Fe₃O₄@SiO₂) particles are synthesized via a solvothermal method. Characterization of the particles defines them to be ~200 nm in diameter with a large surface area (141.89 m²/g), possessing superparamagnetic properties and exhibiting high saturation magnetization (38 emu/g). The synthesized Fe₃O₄@SiO₂ nanoparticles are exploited in the DNA quantification assay and, as predicted, the nanoparticles provide better sensitivity than commercial microscale Dynabeads^® for quantifying DNA, with a detection limit of 4 kilobase-pair fragments of human DNA. Their utility is proven using nanoparticle DNA quantification to guide efficient polymerase chain reaction (PCR) amplification of short tandem repeat loci for human identification.