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[Preprint]. 2024 May 25:2023.07.14.549009. Originally published 2023 Jul 15. [Version 2] doi: 10.1101/2023.07.14.549009

Figure 1.

Figure 1.

DNA sequence specificity of GAF-DBD is kinetically defined. a, Domain map of GAF. 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 zoomed in 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 grey. e, Zoomed-in view of binding events boxed in c. “*” indicates 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 non-cognate sequence. g, Binding frequency of GAF-DBD to cognate or non-cognate DNA. h, Dwell time of GAF-DBD on cognate or non-cognate DNA. Error bars show standard deviation of three technical replicates.