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The effects of distance on inhibition of TBP binding to the TATA box by polyamide 3. Shown is a graphical representation of footprint analysis of polyamide inhibition plotted as fraction of DNA bound (normalized to the fraction of DNA bound in the absence of polyamide) versus polyamide concentration. (A) Upstream constructs. (B) Downstream constructs. (C) Polyamide-binding affinity in the presence and absence of TBP for the D+6 construct.
