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The demand for safer and more efficient non-viral gene vectors has increased with the recent progress of genetic medicine. Appropriate nanocomplex assembly of DNA and gene carriers is critical for successful cellular entry and transfection. However, there is a lack of knowledge on this self-assembly process, let alone the controllability of monodisperse nanocomplexes. This paper describes a novel platform integrating nanobiophotonics (quantum dots-mediated FRET) and microfluidic technology to determine binding kinetics that govern the structural and chemical properties of DNA nanocomplexes. We anticipate that this method will elucidate mechanistic and kinetic insights into the self-assembly process of nanocomplexes which may facilitate the rational design of more efficient gene carriers. In addition, a microfluidic platform offers many advantages, including small volume, fast response to external stimulations, continuous monitoring and real-time control of reaction environments, which may be potentially used to generate more monodisperse complexes.