(A) GST pull-down of double-stranded (ds) DNA oligonucleotides by GST-dTAF2 fragments. Top, the GST fusions (G: GST alone). Middle, the four DNA fragments tested, which are parts of the SCP1 (Juven-Gershon et al., 2006) used in this study (sequence shown, with the TATA, Inr, and DPE elements, from left to right, underscored). Bottom, DNA staining raw images (left) and bar representation of the bound/unbound DNA signals (right). (B) Binding of nuclease-treated GST-dTAF2 (1125–1221) to the lead compound 1 (ChemDiv 7241-4207) printed in quadruplicates in the microarray (yellow rectangle), and its rescue by a double-stranded (ds)DNA oligonucleotide (1 µg/ml) or heparin (2 µg/ml). GST antibody was used for detection. Recombinant GST-dTAF5 was used as a negative control. (C) DNase I footprinting assay on TFIID-promoter binding, in the presence of the lead compound (1, ChemDiv 7241-4207), a structural analog (2, Princeton OSSK_462080), or an unrelated, non-specific (NS) inhibitor (Maybridge BTB08547, see Figure 5—figure supplement 1B). Shown is the digestion product of the end-labeled DNA template separated by gel electrophoresis. The DNA template contains the SCP1. Black boxes depict the positions of the TATA, Inr, and DPE elements, respectively. Blue bracket indicates the ‘footprint’ of TFIID. For simplicity, only two bands (denoted by arrowheads), which were protected (A) or intensified (B) upon TFIID binding, were selected for quantification (right).