We have developed a novel quantum dot (QD) enabled copy number variation (CNV) quantification assay. Current CNV detection techniques are not able to reliably quantify less than a twofold difference. The assay employed a QD to physically transform the target copy number into different electrophoretic mobility (EM) levels that could be assessed by the electrophoresis. We built a model to predict the electrophoretic migration and explain the band broadening of the QD-DNA nanocomplex. The nanoassay demonstrated a remarkable resolution, capable of distinguishing a 1.1-fold (~9%) difference in target copy number. We applied the nanoassay to detect the CNV of the Rsf-1 gene that played an important role in the ovarian cancer.