Magnetophoretic lab on a chip technologies are rapidly evolving into integrated systems for the identification of biomarkers and cells with ultra-high sensitivity. We demonstrate the highly efficient detection of the Human herpes simplex virus type 1 (HSV) UL27 gene through the programmed assembly of superparamagnetic (SPM) nanoparticles based on oligonucleotide hybridization. The state of assembly of the SPM nanoparticles was determined by optical signature of the synchronized motion on the beads on a micromagnetic array (MMA). This technique has been used to identify <200 copies of the HSV UL27 gene without amplification in less than 20 minutes. The MAA can also be used to separate gene-SPM bead aggregates from millions of unreacted SPM beads based on nonlinear magnetophoresis (NLM). The MMA-optical detection system promises to enable highly sensitive, nucleic acid analysis to be performed without amplification and with the consumption of minimal amounts of reagent.