Extended Data Fig. 3: Genome-wide mapping of binding sites of 9 in cells under light illumination.
From: Optical control of gene expression using a DNA G-quadruplex targeting reversible photoswitch
a, FID curves for G4 MYC and dsDNA induced by increasing concentrations of non-illuminated and 405 nm illuminated G4switch-biotin. The apparent Kd of tran-G4switch-biotin for G4 MYC is 0.63 ± 0.02 µM, derived from its normalised DC50 (1.58 ± 0.05 µM) (See Methods), while Kd values for other conditions were not determined within the molecule concentration range (0-5 µM). Results are shown as mean ± s.d. from four replicates (n = 4). b, Differential binding analysis of the union of Chem-map binding sites across all replicates (three biological replicates, each with three technical replicates) for both isomers of 9 shows 17,957 significantly differentially binding sites of trans-9 compared to the cis isomer. Dots highlighted in red represent binding sites that are significantly different (FDR < 0.05) between the two isomers. Positive fold changes indicate an increase in trans-9 binding. c, FRiP analysis comparing the Chem-map profiles of 9 between the 405 nm illuminated trans form and non-illuminated cis form in U2OS cells. Results represent the mean ± s.d. from three biological replicates, each with two technical replicates (n = 6). ****P < 0.0001, two-tailed unpaired t-test. d,e, Differential binding analysis displaying changes in 405 nm illuminated 9 Chem-map binding events across the union of all three biological replicates for pre-treatment with (d) 4 µM and (e) 20 µM PDS, compared to the vehicle DMSO for 3 h in U2OS cells. Dots highlighted in red represent significantly changing sites (FDR < 0.05) between DMSO and PDS treatments. A positive fold change indicates a decrease in 405 nm illuminated trans-9 binding.
