Assays of metabolites and disease biomarkers with high sensitivity are most demanding in the fields of medical and biological sciences. To accomplish this goal, the use of magnetic particles (MPs) has been attractive mainly due to their distinct advantages, including facile control by magnetism, high biocompatibility, and high detection sensitivity. In particular, integration with microfluidic systems endowed the MP based assay with significantly enhanced sensitivity and selectivity in detecting target analytes. In addition to the combination of a microfluidic system, modulations in the structure and shape of MPs are expected to confer enhanced analytical performance on the MP-based assay. Here a Magnetophoretic assay based disease biomarker detection was demonstrated. Firstly, the system was applied to detection of allergen specific IgE in patient serum, and the performance of the system was compared with Pharmacia CAP system and 10 fold sensitivity enhancement was found. Secondly, the magnetic nanoparticles used for the magnetophoretic assay system was engineered to have dual functionality, which would enable it to cluster to larger magnetic nanoclusters, it was found that the formed magnetic nanoclusters would endow the system with two orders of magnitude sensitivity enhancement to magnetic nanoparticles alone was used when a prostate specific antigen (PSA) was used as a model system. Finally, a new form of magnetic nanocluster was constructed by using DNA and DNA binding protein to linearly assemble magnetic nanoparticles along the DNA. This form of magnetic nanocluster is expected to find its application in the field of simultaneous diagnosis and gene therapy.