Joule heating is a primary limitation in the slab gel electrophoresis which is a gold standard method in biochemistry and biotechnology. In this paper, we introduced an innovative new class of heat transfer nanocomposite engineered by inclusion of metal oxide nanoparticles (NPs) in conventional separation medium (gel). The nanocomposite exhibits high thermal conductivity compared to gel itself. The results suggest a unique correlation between average particle size and thermal conductivity of metal oxide NPs with resolution improvement of the separation, i.e. reduction in Joule heating. Ceria, zirconia, tungsten oxide, and lanthania NPs were loaded into the agarose gel separately and used as a separation medium for gel electrophoresis. Among the NPs, ceria with the smallest size (5.2 nm) and highest thermal conductivity (17 W m -1 K -1 ) presented a better performance in reduction of Joule heating. By loading 0.3 % (m/v) ceria, zirconia, and tungsten oxide NPs into the agarose gel at 25 °C , the thermal conductivity of gel increased 79, 78, and 78 %, and resulted in 22, 18, and 14 % reduction in Joule heating (230 V), respectively. The overall separation efficiency and resolution increased for agarose/zirconia gel as compared with those of pure agarose gel. For example, the separation efficiency of 70 and 80 (bp) peaks increased 260 and 165 %, respectively. Also, the resolution increased from 1.65 for pure agarose gel to 6.32 for agarose/zirconia gel.