Figure 3.

Nucleosome blocks GAF-DBD 1D sliding to SHL5 and deeper locations into the nucleosome core. a, Schematics of nucleosome constructs where the nucleosomal Cy7-labeled cognate motif (in blue) is placed at SHL7, SHL5, or SHL3 location and the other Cy5-labeled cognate motif (in red) is on the linker DNA. The nucleosome is positioned by the Widom 601 sequence flanked by 40 bp linker DNA on both sides. b-d, Representative single-molecule trajectories of Cy3-GAF-DBD binding to linker or nucleosomal motifs on the SHL7 (b), SHL5 (c) and SHL3 motif (d) nucleosome constructs. e-g, Binding site locations for GAF-DBD binding events on nucleosome constructs where Cy7-labeled motif is located at SHL7 (e), SHL5 (f) or SHL3 (g) location. h, GAF-DBD binding behavior categories on each nucleosome construct. i, Categories of 1D diffusion behaviors on the SHL7 construct. j, GAF-DBD dwell times on the Cy7-SHL7 motif, Cy5-linker motif and nonspecific sites on the SHL7 construct.