DNA microarray of non-viral reverse transfection in cell engineering allows drastic downsizing of large-scale functional screening of genes and siRNAs. However the control of localizability and efficiency of the microarray is still considered as a critical barrier in practical use. One of the major breakthrough to increase the transfection efficiency may be control in the condition of DNA/transfection reagent complex on the microarray surface. In this paper, we showed that negatively charged gold colloid (GC) is successfully used to control the DNA/reagent complex on a glass surface. The conjugation of gold nanoparticles (20 nm in diameter) to the pEGFP-N1/JetPEI complex resulted in a more than 2.5-fold increase in the intensity of fluorescence of enhanced green fluorescent protein (EGFP) (based on the efficiency of transfection) from human mesenchymal stem cells (hMSCs), as compared to the control without GC. Our method for reverse transfection should be useful not only for cell array-based analyses but also as a novel gene-delivery method for gene therapy in regenerative medicine.