Extended Data Fig. 4: Nucleosomal motif accessibility depends on helical phasing.
From: GAGA zinc finger transcription factor searches chromatin by 1D–3D facilitated diffusion
a, Representative native PAGE gels for nucleosome constructs used in this study. All nucleosome constructs used in this study were assessed by native PAGE gels and showed similar results. b, Classification of Cy3-GAF-DBD binding events on ‘601’ nucleosomes (40-N-40) with a cognate site placed at SHL6.5, SHL4.5, and SHL2.5. Classification is based on Cy3-Cy7 FRET dynamics, see details in methods. c, Classification of Cy3-GAF-DBD binding events on same ‘601’ (40-N-40) nucleosomes with cognate site placed at SHL7, SHL5, and SHL3 (same dataset as Fig. 3, re-analyzed for direct comparison with a). d, Representative single-molecule trajectories for each category of 601-SHL6.5, -SHL4.5, and -SHL2.5 nucleosomes. Some scanning events show prolonged Cy3-Cy7 FRET (right) which appear distinct from scanning events on the 601-SHL7 nucleosomes (Fig. 3b). Note that scanning events (events that show dynamic Cy3-Cy7 FRET) may also come from free DNA which contaminates the nucleosome sample.
