Herein we report three novel methods which utilize chemical conjugated magnetic beads to purify synthetic gene from its synthesis solution and prepare the synthesized gene in suitable buffer for downstream applications. Silica-coated magnetic beads are applied for non-specific DNA purification to remove short oligonucleotides and monomers. Streptavidin conjugated magnetic beads and (dT)<sub>25</sub> Oligo immobilized magnetic beads are introduced for specific DNA extraction. The performances of these methods are investigated and compared using gel electrophoresis. The optimal conditions for enhancing the extraction efficiency are discussed. In addition, the approach to integrate these solid-phase purification methods into microfluidic devices is presented.