The potential of utilizing the DNA binding protein lac repressor (LacI) to organize inorganic nanoparticles (NPs) is explored in this study. A peptide cognitive of both SiO2 and TiO2 simultaneously (STB1, -CHKKPSKSC-) is genetically engineered into the C-terminus of LacI to give LacI-STB1, and the inserted STB1 peptides in the context of LacI-STB1 molecules are shown to actively interact with both SiO2 and TiO2. Wild-type LacI is found to interact with the two surfaces at its flexible N-terminal DNA binding domain, and LacI-STB1 exhibits much stronger binding affinity to both surfaces by harnessing a second binding region (STB1 peptide) fused at its C-terminus. The quantitative analysis of binding kinetics reveals that, compared to wild-type LacI with one binding region (N-terminus), two remote binding regions (N-terminus and C-terminus) in LacI-STB1 do not lead to faster adsorption rates to the two surfaces, but remarkably slow down the desorption rates. Finally, using LacI-STB1 as a linker, the successful assembly of a sandwich nanostructure of DNA/LacI-STB1/TiO2 NPs is demonstrated using surface plasmon resonance (SPR) measurements and TEM. The demonstrated LacI-STB1-mediated assembly of TiO2 NPs on DNA scaffold may provide a generic platform for controlled spatial arrangement of various nanoparticles of engineering interest.