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Electrostatic self-aligned positioning of a single 7 nm nanoparticle in the cage-shaped protein ferritin onto an aminosilane disk pattern as large as next-generation photolithography can produce is demonstrated. Genetic modification of the ferritin increased its surface charge density and therefore improved its electrostatic interaction. Single molecules of the recombinant ferritin could achieve self-aligned placement on 32–45 nm disks under the optimal solution condition, which was calculated by numerical analysis. This biological self-aligned placement, incorporated into next-generation photolithography techniques, will be a useful wafer-scale nanofabrication tool.