Peptide microarrays are becoming a promising alternative to protein microarrays due to the challenges associated with protein immobilization and purification. Here, we put forward a novel experimental-based approach that combines DNA-directed immobilization, nanografting, and atomic force height measurements to immobilize computationally designed cyclic peptide on an ultra-flat gold substrate. This procedure yields peptide-DNA nanoarrays, which can bind to the solvent-exposed site on the Beta-2-microglobulin (β2m).