Fig. 2.
CSI profile of PA1. (A) Structure of polyamide-Cy3 conjugate PA1 (ImPy*PyPy-γ-ImPyPyPy-β-Dp). (B) Histogram of averaged intensities of all replicate features. Intensities are background-subtracted so that the mean intensity is zero. Red numbers indicate Z scores. (C)(Top) Logo (53) based on the sequences from the top Z score bin (Z >25). (Middle) DNA sequence that would be targeted by PA1 based on the ring pairing rules for polyamides; an Im/Py ring pair targets G·C, and a Py/Py pair targets either A·T or T·A (2). Numbers indicate base pair positions. (Bottom) A ball-and-stick schematic of PA1. Im or open circle, N-methylimidazole; Py or filled circle, N-methylpyrrole ring; Py* or open circle with inner dot, N-methylpyrrole ring with a Cy3 dye attached; β or diamond, β-alanine; Dp or a half circle with a positive charge, dimethylaminopripylamide; γ or turn, γ-aminobutyric acid. (D) Intensity profile of all sequence permutations of the core consensus sequence 5′-WGWWCW-3′. The intensities of all probes that contain a specific permutation of the core consensus sequence are averaged together. (E) Plot of the correlation between CSI intensities and equilibrium association constants (Ka) determined from nuclease protection (DNase I footprinting) experiments (Table 1). The intensities of all CSI probe sequences that contain a particular footprinted sequence are averaged together.