RATIONALLY DESIGNED BENZYL-N-METHYL)AMINOCARBONYL]-1,3-DIAMINOBENZENE, BIGBEN, BINDS TO THE MINOR-GROOVE OF D(CGCGAATTCGCG)(2) AS DETERMINED BY 2-DIMENSIONAL NUCLEAR-MAGNETIC-RESONANCE SPECTROSCOPY

We have used homonuclear NMR techniques to investigate the interaction s between the de novo designed minor groove ligand N,N'-bis[(N-p-guani dinobenzyl-N-methyl) aminocarbonyl]-1,3 -diaminobenzene ''BIGBEN'' and the receptor for which it was designed, the d(CGCGAATTCGCG)(2) dodeca mer. Our NMR results show unequivocally the interaction between the no nexchangeable and exchangeable protons of BIGBEN and the minor groove protons of the dodecamer. These interactions were characterized with t he use of 1D NMR titrations to establish that the ligand is in fast-ch emical exchange with the dodecamer on the chemical shift time scale, h omonuclear NOESY experiments to establish the connectivities between t he ligand and the DNA, and NOE-assisted computational modeling to deve lop 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 ther e is high-resolution structural data. A structural database is then se arched for putative ligands which may have shape complementarity to th e desired binding site on the receptor. The ligand, or a derivative th ereof, is synthesized, and its ability to bind to the desired receptor is tested. The cycle culminates with the characterization of the stru ctural interactions in the complex, elucidated here for BIGBEN and the dodecamer d(CGCGAATTCGCG)(2).