We propose to synthesize new sequence specific DNA binding molecules for double helical B-form DNA. The methods of analyses for the sequence specificity of these synthetic DNA binders are footprinting and affinity cleaving techniques which allow visualization of the DNA binding sites on 32P end-labeled restriction fragments by high resolution gel electrophoresis. In the next funding period we will synthesize hepta, octa, nona and deca-N-methylpyrrolecarboxamide-EDTA.Fe(II) and ask how these oligo-N-methylpyrrolecarboxamides fit the natural curvature of the DNA helix. We will use a C4 diamide linker as a hinge to connect two hexa-N-methylpyrrolecarboxamide-EDTA.Fe(II) molecules and ask whether we can achieve 15 base pair recognition at pure A.T sequences. We will synthesize oligobenzimidazoles to develop alternative recognition elements for A.T rich DNA sequences. We will synthesize and study two potential """"""""G+C words or recognition elements"""""""" and tether these to the tris-N-methylpyrrolecarboxamide 5 bp A.T recognition element. One of these G+C words is the bithiazole derived from bleomycin and the other is the chromophore from olivomycin. In an effort to control orientation of the oligo-N-methylpyrrole in the minor groove of A.T rich sequences we will introduce a chiral enantiomerically pure center to test for a diastereomeric discrimination of orientation on the right-handed DNA helix. We will study the sequence specific alkylation of DNA by such molecules as bromo-N-acetyldistamycin and higher homologs, a potential class of highly specific DNA cleaving molecules. We will initiate an exploratory program aimed at the sequence specific O-alkylation at phosphate as another method of backbone cleavage of DNA. We will initiate an exploratory effort aimed at the sequence specific photoalkylation of DNA in the major groove. Finally, we will synthesize and study the use of spermine-EDTA.Fe(II) as a sequence neutral DNA cleaving agent, perhaps a new useful tool for nucleic acid research.
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