In this work, we investigate micro-capillary electrophoresis (mu-CE) using monodispersed SiO2 nanoparticles added to an electrophoresis buffer solution to obtain high mobility and high separation of double-strand DNA. Various particle sizes of monodispersed SiO2 nanoparticle solutions were mixed with conventional 0.7% hydroxyl propyl methyl cellulose (HPMC) buffer solution to achieve mu-CE. We achieved perfect separation of the DNA specimen (100 bp to 1.5 kbp) at a certain SiO2 nanoparticle size. In addition, we discuss the effect of SiO2 nanoparticles during electrophoresis.