AT SELECTIVITY AND DNA MINOR-GROOVE BINDING - MODELING, NMR AND STRUCTURAL STUDIES OF THE INTERACTIONS OF PROPAMIDINE AND PENTAMIDINE WITH D(CGCGAATTCGCG)(2)

A molecular modelling strategy has been developed to identify potentia l binding sites for bis(amidine) ligands in the minor groove of duplex DNA. Calculations of interaction energy for propamidine and pentamidi ne with d(CGCGAATTCGCG)(2) show that this duplex contains two symmetri cally equivalent binding sites of identical affinity, each displaced b y 0.3-0.4 bp from the centre of the AT segment. The ligands occupy gro ove sites spanning similar to 4 and 4-5 bp, respectively, with asymmet ric binding to the 5'-AATT sequence. The DNA-bis(amidine) interactions have been examined by high-resolution H-1-NMR. The patterns of induce d changes in DNA proton chemical shift and the DNA-ligand NOEs confirm that both agents bind in the AT minor groove in a non-centrosymmetric fashion. Detailed structures were determined for each complex using a NOE-restrained simulated annealing procedure, showing that the B-type DNA conformation is not significantly altered upon complexation with either ligand. The free]DNA duplex has previously been shown to be ext ensively hydrated in the minor groove [Kubinec, M.G. and Wemmer, D.E. (1992) J. Am. Chem. Sec. 114, 8739-8740; Liepinsh, E., Otting, G. and Wuthrich, K. (1992) Nucleic Acids Res. 20, 6549-6553]. We detect hydra tion water close to the A(H2) protons in the presence of propamidine, which may stabilise certain waters against exchange. This conclusion s upports recent crystallographic analyses, suggesting that such ligands may use water molecules to bridge between amidinium protons and host DNA bases. Details of the ligand interactions with AT-tract DNA duplex es can now be compared for the subsequences 5'-AAT, 5'-AATT and 5'-AAA TTT.