Fig. 2: GAF-DBD explores free DNA by 1D diffusion.
From: GAGA zinc finger transcription factor searches chromatin by 1D–3D facilitated diffusion
a, Three-color smFRET experiment distinguishes whether GAF-DBD is bound to Cy7-labeled site 1, Cy5-labeled site 2 or a nonspecific site on Drosophila hsp70 promoter DNA. b, A single-molecule trajectory shows GAF-DBD sliding back and forth on the DNA between two cognate motifs. Binding site assignment is shown below as a colored ribbon. c, A total of 50 binding events shown as a rastergram. d, Zoomed-in view of the boxed region in b. e, GAF-DBD dwell times for motif-specific binding (τmsb) on site 1, site 2 or nonspecific site on the DNA with regular (6.25 mM, n = 51 traces) or low (3 mM, n = 32 traces) MgCl2. The concentration of GAF-DBD used in these experiments was 0.1 nM. Error bars represent 95% confidence intervals. f, Schematic of GAF-DBD sliding on DNA. Circles represent GAF-DBD. Green circles, GAF-DBD binding to a nonspecific site; blue circle, GAF-DBD binding to site 1; red circle, GAF-DBD binding to site 2.
