The rational organization of transition metal ions that have unpaired electrons can lead to nano-scale systems with magnetic and electronic properties useful for nanotechnology and molecular electronics applications. We use as scaffold for the organization of transition metal-ion peptide nucleic acid (PNA), a synthetic analog of DNA that forms helical duplexes by Watson-Crick hybridization. The incorporation of ligands in complementary PNA oligomers makes possible the formation of a duplex that binds metal ions at predefined locations.