Design of nucleosome templates with p53BS. (A) A 217-bp dsDNA library was designed containing p53BS in various nucleosomal positions. Nucleosomes were formed and purified, generating a nucleosome library that was incubated with increasing amounts of TP53 protein. TP53–nucleosome complexes were separated by EMSA, and the bound and unbound DNA was recovered, quantified by qPCR, and sequenced. (B) A 20-bp-long p53BS (low and high affinity) was placed at different positions 0, 5, 41, 46, 66, 71, and 81 bp away from the dyad. The superhelix location (SHL) is designated for each nucleosome sequence. (C) Within the nucleosome, three different positions (dyad, intermediate, and edge) were chosen with increasing distance to nucleosome dyad.
