Fig. 4: 3D diffusion dominates for inner nucleosomal targets.
From: GAGA zinc finger transcription factor searches chromatin by 1D–3D facilitated diffusion
a, Drosophila hsp70 promoter nucleosome construct (0-N-40, same DNA as in Extended Data Fig. 3f) for investigating GAF-DBD search when two binding sites lie within the nucleosome core. b,c, Representative single-molecule trajectories for site A (b) and site B (c) binding (0.4 nM GAF-DBD used). d, Binding event categories on the nucleosome. e, A 1 − CDF plot of motif dwell times for nucleosome (orange) compared to free DNA (blue). Fitted τ values are provided in Supplementary Table 5. Free DNA data are aggregated from Cy7–dyad site and Cy5–edge site dwell times on the same DNA template (Extended Data Fig. 3f). f, EMSA for GAF-DBD binding to Cy5–hsp70 NCP. g, EMSA showing GAF-FL binding to Cy5–hsp70 NCP. h, EMSA showing GAF-FL binding to Cy5–hsp70 DNA (the same DNA for Cy5–hsp70 NCP). EMSA experiments in f–h were independently repeated at least once with similar results.
