We generated the feasibility of DNA separation in free-solution using genetically engineered repetitive polypeptides as drag-tags. Two different-sized repetitive polypeptides were designed, expressed in E. coli, and purified. They were conjugated to a fluorescently labeled DNA (100 base), and the electrophoretic mobilities of these conjugate molecules were analyzed on a microchip. The results of these studies indicate that genetically engineered repetitive polypeptide is a prominent candidate for rapid and high-throughput genetic mutation detection, such as SNP analysis.