We have used homonuclear NMR techniques to investigate the interactions between the de novo designed minor groove ligand N,N’-bis[(N-p-guanidinobenzyl-N-methyl) aminocarbonyl]-1,3 -diaminobenzene "BIGBEN" and the receptor for which it was designed, the d(CGCGAATTCGCG)(2) dodecamer. Our NMR results show unequivocally the interaction between the nonexchangeable and exchangeable protons of BIGBEN and the minor groove protons of the dodecamer. These interactions were characterized with the use of 1D NMR titrations to establish that the ligand is in fast-chemical exchange with the dodecamer on the chemical shift time scale, homonuclear NOESY experiments to establish the connectivities between the ligand and the DNA, and NOE-assisted computational modeling to develop a structural interpretation of the data. This represents the first complete iteration of our design cycle applied to the minor groove of DNA. The cycle begins with the selection of a receptor for which there is high-resolution structural data. A structural database is then searched for putative ligands which may have shape complementarity to the desired binding site on the receptor. The ligand, or a derivative thereof, is synthesized, and its ability to bind to the desired receptor is tested. The cycle culminates with the characterization of the structural interactions in the complex, elucidated here for BIGBEN and the dodecamer d(CGCGAATTCGCG)(2).