Fig. 5.

PRDM9 binding to different lengths of DNA. a In this competition EMSA, 250 nM PRDM9^Cst-ZnF (YFP tagged) was incubated simultaneously with hot (biotinylated) reference DNA (75 bp Hlx1 ^B6) and different ratios of excess cold Hlx1 ^B6 for 1 h (a time frame that showed unchanged complex amounts; Supplementary_Fig_S4). We used for each experiment different lengths of cold DNA (75 bp, 39 bp, 34 bp, 31 bp, 28 bp-d, and 28 bp-u sequences are shown in Supplementary_Table_S1, section C) representing truncations of the 75 bp Hlx1 ^B6 sequence. Shown are representative EMSAs for the cold competitors with 31 and 28 bp. The measurements were performed in triplicates for each cold competitor. b Intensities of the shifted bands are calculated relative to the reference PRDM9^Cst-Hlx1 ^B6 complex without the addition of cold DNA (lane 2) and are plotted as relative intensities against the concentration of the cold competitor in a semi-logarithmic graph. 28 bp-d and 28 bp-u indicate 28 base-pair long fragments with truncations of three bases from the target binding site at either the downstream (3′ end) or the upstream (5′ end) end, respectively