Fig. 1: DNA sequence specificity of GAF-DBD is kinetically defined.
From: GAGA zinc finger transcription factor searches chromatin by 1D–3D facilitated diffusion
a, Domain map of GAF. ZF, zinc finger. b, Schematics of two-color smFRET experiment to measure cognate-specific binding of GAF-DBD. c, Single-molecule trajectories showing Cy3–GAF-DBD binding to Cy5–DNA containing a GAF cognate site. Boxed binding events are magnified in e. Examples of dwell time measurements (t) are shown on the third trajectory. d, Representative single-molecule trajectories of Cy5–cognate DNA bound by Cy3–GAF-DBD showing an initial donor-only period before acceptor signal increases. The donor-only period is highlighted in gray. e, Zoomed-in view of binding events boxed in c. The asterisk indicates a transient Cy3-only fluorescence spike during binding. f, Single-molecule trajectories showing Cy3–GAF-DBD nonspecifically binding to Cy5–DNA where the cognate site was substituted with a noncognate sequence. g, Binding frequency of GAF-DBD to cognate or noncognate DNA. h, Dwell time of GAF-DBD on cognate or noncognate DNA. Error bars show the s.e.m. from mean binding frequencies of technical replicates (cognate DNA, three replicates, total n = 317; noncognate DNA, two replicates, total n = 282). The concentration of GAF-DBD used in these experiments was 0.2 nM. Fluor., fluorescence.
