AT selectivity and DNA minor groove binding: modelling, NMR and structural studies of the interactions of propamidine and pentamidine with d(CGCGAATTCGCG) 2

Abstract

A molecular modelling strategy has been developed to identify potential binding sites for bis(amidine) ligands in the minor groove of duplex DNA. Calculations of interaction energy for propamidine and pentamidine with d(CGCGAATTCGCG) 2 show that this duplex contains two symmetrically equivalent binding sites of identical affinity, each displaced by 0.3–0.4 bp from the centre of the AT segment. The ligands occupy groove sites spanning ∼4 and 4–5 bp, respectively, with asymmetric binding to the 5′-AATT sequence. The DNA-bis(amidine) interactions have been examined by high-resolution 1H-NMR. The patterns of induced 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 extensively hydrated in the minor groove [Kubinec, M.G. and Wemmer, D.E. (1992) J. Am. Chem. Soc. 114, 8739–8740; Liepinsh, E., Otting, G. and Wüthrich, K. (1992) Nucleic Acids Res. 20, 6549–6553]. We detect hydration water close to the A(H2) protons in the presence of propamidine, which may stabilise certain waters against exchange. This conclusion supports 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 duplexes can now be compared for the subsequences 5′-AAT, 5′-AATT and 5′-AAATTT.