Fig. 1: DSB repair-related proteins bind ODNs in a sequence-biased manner.

a Schematic overview of ODIP-Seq for capturing preference binding sequences of the protein of interest. The ODN pool was incubated with the cell lysate for 12 h, and the ODN-protein complexes were immunoprecipitated using the corresponding primary antibody. The ODNs were then recovered from the beads using the proteinase K-phenol-chloroform method, and a library was prepared for next-generation sequencing. ODIP, oligodeoxynucleotide immunoprecipitation. b Heatmap of relative TPM of precipitated ODNs with RAD51, RAD50, Ku80 and CtIP. Relative TPM for each ODN was calculated using the mean of two independent replicates. c Violin plots showing the overall relative TPM distribution of precipitated ODNs with the indicated DNA repair proteins. The white dot represents the median. The box spans from the 25th percentile (first quartile) to the 75th percentile (third quartile). The whiskers extend to the smallest and largest data points within 1.5 times the interquartile range (IQR). d, e Characterization of top-ranked ODNs bound to the RAD51 (d) or Ku80 (e) protein in Fig. 1b using the WebLogo 3 website. f, g Evaluation of the binding activity of RAD51 protein with top- and bottom-ranked SSO by biotin-ODN pulldown assay (f) and ODIP assay (g). The digits denote the number of SSOs. h, i Evaluation of the binding activity of Ku80 protein with top- and bottom-ranked SSO using biotin-ODN pulldown assay (h) and ODIP assay (i). The digits denote the number of SSOs. Data are representative of 3 independent experiments (f–i). The sequences of all SSOs used are shown in Supplementary Data 3. Source data are provided as a Source Data file. Figure a Created with BioRender.com released under a Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International license.