We propose to use high resolution proton two dimensional NMR structural and hydrogen exchange techniques to monitor complex formation between a series of antitumor agents and their sequence specific binding sites on deoxyoligonucleotides of defined sequence. The antitumor agents form a diverse class and include the bis-intercalating quinoxalines echinomycin and triostin which bind at dC-dG sites and TANDEM which binds at dT-dA sites. The experiments will probe for Hoogsteen base pair formation adjacent to the binding site and monitor the propagation of such perturbations along the helix. The aureolyic antitiumor agents chromomycin and mithramycin recognized and complex to dG-dG sites and we shall attempt to distinguish between potential intercalative and groove bindign modes, as well as establish intermolecular interactions involving the five attached hexapyranoses. The athracycline antitumor agents nogalamycin and bis(diethylamino)ethylamino) substituted anthraquinones are known to intercalate into DNA at alternating pyrimidine-purine sequences. We shall attempt to establish the overlap geometries at the intercalation site, the orientation of the bulky side chains in the minor and major grooves and the intermolecular interactions that stabilize the complex. The above studies will be undertaken on oligonucleotides extending from tetranucleotide to decanucleotide duplexes and attempts will be made to quantitate the nuclear Overhauser effect based distance constrains to define intermolecular interactions in the complex. These NMR experiments will be extended to binding studies of synthetic oligo(N-methylpyrrolecarboxaminde)s and their chiral analogs to A.T rich regions in oligonucleotide duplexes to check the principle of bifurcated hydrogen bonding, as well as rules governing chiral recognition in intermolecular interactions. Studies will also be undertaken on lexitropsins where the pyrrole specificity for A.T base pairs is replaced by imidazole specificity for G.C base pairs. Finally, the separate and simultaneous binding of two antitumor agents on adjacent sites of oligonucleotide duplexes will be investigated to probe for synergistic binding associated with combination chemotherapy.
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