Fig. 6: MH selected by Pol θ usually contains mismatches.

a Diagram of base pairing positions P1–P6 of a MH. In this example, P1–P4 are matched, and P5–P6 are mismatched. b Heatmap showing read count percentage for each MH type utilized by Pol θ Δcen in the indicated libraries prepared with different oligo pools and a blocked bottom oligonucleotide (Oligo 10). MH <6 bp means the MH is anchored within 5 nucleotides of the 3′ end of the bottom strand. MH matched base pairs (0–6) indicates that the MH contains 0–6 matched bases. c Cluster plot of the favored MH used by Pol θ Δcen for end-joining reactions. All anchoring positions for Library 6–10 oligonucleotide pools (blocked bottom “Oligo 10”) were analyzed. If an oligonucleotide used the same MH in more than 50% of the read counts, it was designated a favored MH. Each column corresponds to one of these 910 individual oligonucleotides having a favored MH. Rows correspond to positions P1 to P6 of the MH as in panel (a). The percentage of matching at each position in the favored MH is indicated with a blue color scale. Mismatched positions are white. d Matching at position P1 of an MH is favored by Pol θ for anchoring and extension during initiation of end-joining. The fraction of matches or mismatches at 35 P1 positions (blue dots and box plot) is compared with theoretical fractions (red dots). Box plots show the median (center line), the 25th and 75th percentiles (bounds of box), and Tukey whiskers (1.5X interquartile range). The statistical significance is labeled with the p value derived from a unpaired two-sided t-test. e MH containing >2 matches show higher anchoring frequencies than theoretical frequencies. Experimental anchoring frequencies of five different types of MHs at 35 positions are shown with green dots and the mean ± standard deviation in blue. The comparison with theoretical frequency (red dots) was done with a two-sided t-test. The resulting p value is shown; ns indicates no significant difference. Source data are provided as a Source Data file.