The long term objective of this research is to provide a detailed understanding at the molecular level on the DNA binding of some model ligands through which rational designs of effective anti-cancer drugs can hopefully be based. This proposal will focus on the sequence specific binding and possible synergistic effects of three antibiotics having distinctly different DNA binding models: actinomycin D (ACTD), a guanine- specific intercalator, chromomycin A/3 (CHR), a guanine-specific minor groove binder; and distamycin A (DST), an A:T-specific minor groove binder. Our immediate goals for the next four years will be: (1) To refine our understanding on the base sequence specific DNA binding of ACTD by: (a) studying the effects of flanking base mismatches on the binding affinity and kinetic behaviors of the classic GpC sequence; (b) investigating the drug-induced conformation shifts in some DNA oligomers (allosterism); (c) elucidating possible DNA conformational alterations at one region due to a ligand binding at a proximal location (telestability); (d) delineating ACTD binding to DNA oligomers which contain no GpC sequence; and (e) obtaining detailed structural and binding information via NMR studies with certain DNA oligomers and their drug complexes. (2) To elucidate the DNA base sequence specificity of CHR at the non-self- complementary tetranucleotide levels. (3) These goals are to be achieved via systematic spectral titrations (absorbance, circular dichroic; fluorescence and NMR), association and dissociation kinetic measurements, optical and calorimetric melting experiments, and gel electrophoretic pattern analysis. DNA oligonucleotides of appropriate length and sequence will be used in these studies.
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