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All relaxation reactions were run at a sufficiently high (and constant) binding site-to-polyamide ratio to ensure that unwinding effects were only caused by sequence-specific interactions.
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The 60 amino acid sequence (222-281) of GCN4 contains the 'leucine zipper' dimerization domain and the 'basic region' responsible for DNA binding.
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The effects of polyamide-acridine conjugates binding only to the upstream site showed similar GCN4 inhibition values as ARE-41.
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