Interaction of minor-groove-binding diamidine ligands with an asymmetric DNA duplex. NMR and molecular modelling...

The aromatic diamidines berenil and propamidine bind reversibly to A+T-rich sites in the minor groove of B-form DNA duplexes. Based on extensive solution and crystallographic information we have designed a non-self-complementary double-stranded DNA sequence, d(GCAATGAGCG).d(CGCTCATTGC), that should contain a near-ideal binding site for berenil and a poorer site for the larger propamidine molecule, viz. d(AAT).d(ATT). 1H-NMR studies show that both ligands bind with 1:1 stoichiometry to the embedded 5'-AAT site, and induce numerous shifts of NMR resonances of DNA protons located in the minor groove. In addition, interactions with each strand can be distinguished by NOE spectroscopy due to the inherent asymmetry of the DNA. Detailed modelling based on experimental data show that no significant distortion of the B-DNA duplex is induced by either ligand. Sufficient NOE data were obtained to determine the position of the bound ligands in each complex. These conclusions are in agreement with predictions from molecular modelling calculations that provide a microscopic energy profile for interaction with the minor groove tract. Such calculations reveal an unexpected heterogeneous 5'-ATGA binding site that includes a spanned guanosine. This secondary binding site accounts for the extensive chemical shift perturbation induced by these ligands. The structures of the free DNA and the reversible complexes formed with each ligand molecule have been refined using an NOE-restrained isothermal annealing procedure. These structures confirm that the introduced ligands effect minimal perturbation of the helix, with binding to the 5'-AAT base sequence largely determined by specific non-bonded interactions.