The goal of this project is to improve our understanding of drugs which bind in the minor grove of DNA, with a preference for specific sequences. We will concentrate effort on distamycin-A, which binds to A:T containing sequences of four or more bases, and chemically synthesized analogs of it, that bind sequences which contain one or more G:C pairs in addition to A:Ts. The basis for the sequence preference in these compounds is not well understood, making rational design of analogs targeted to specific sequences difficult. our structural characterizations will be done primarily using NMR spectroscopy, which allows us to distinguish different interconverting complexes in solution, to identify the binding sites, and to determine the kinetics of transfer between different binding sites. we will carry out systematic variation of DNA sequences to determine the effects on recognition by this class of compounds. New chemical variants within this class will be studied, particularly those containing imidazole rings replacing pyroles of the natural distamycin, and those which have four or more linked rings. We will also continue efforts in preparing dimeric drugs which can bind in the side-by-side 2:1 mode. Use of hetero-complexes (a distamycin and a lexitropsin bound in the same site) will also be pursued to achieve not only base pair type selection (G:C vs. A:T), but also orientation selection (G:C vs. C:G). We will also measure the rate of exchange of drug between different binding sites, both inter- and intra-molecularly. Such experiments will help us understand ionic contributions to DNA recognition by small molecule ligands.
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