Fig. 2

Evaluating protein-DNA interaction by electrophoretic mobility shift. a Direct band shift assays for various sequence motifs. The DNA is detected by EtBr staining. The CT probe contains the control TAATCTAATCA sequence and shows a complete shift to the slower-migrating form in the presence of an excess quantity of the DUX4 DNA-binding domain. Other oligos showed various shift efficiencies. b Competitive band shifts of the four flavors of the DUX4 ChIP-seq consensus motif. The CT probe is labelled with FAM; thus, the gel has no EtBr, and binding is competed with unlabeled oligos. All four flavors of the DUX4 ChIP-seq consensus effectively compete away binding to the FAM-CT probe when provided in excess, while the mutant sequence fails to compete. c Competitive band shifts of the sequences tested for direct band shifting (in a, above)