Comprehensive high-Resolution analysis of hairpin polyamides utilizing a fluorescent intercalator displacement (FID) assay

Abstract Four hairpin polyamides bearing subtle N- and C-terminal substitutions were examined in a fluorescent intercalator displacement (FID) assay enlisting a library of 512 DNA hairpins that contain all possible five base pair sequences in a challenging probe of its capabilities for establishing DNA binding sequence selectivity. Not only did the assay define the global sequence selectivity expected based on known structural interactions and Dervan's pairing rules establishing the utility of the method for characterizing such polyamides, but previously unappreciated subtle substituent effects on global sequence selectivity were also revealed. Thus, we report the discovery of a novel five base pair high affinity binding site of the form 5′-WWCWW (vs 5′-WGWWW) for the polyamide ImPyPy-γ-PyPyPy-β-Dp and its structural basis.