Figure 2: Cellular assay for NHEJ of systematically varied end structures.
From: The fidelity of the ligation step determines how ends are resolved during nonhomologous end joining
(a) Description of cellular assay. (b) Joining efficiencies for each substrate, comparing wild-type HCT 116 cells to its LIG4-deficient variant (LIG4−/−). Error bars denote the s.d. for 12 (5′GATC, 5′GCGT) or six (all others) independent electroporations. (c) Substrates possessed end structure varied as shown. Product structures were defined as in Fig. 1a, and the proportion (%) of each determined by sequencing of junctions from wild-type cells, averaged from two libraries, each library from a pool of three electroporations (see also Methods). Error bars represent the range of results from the two libraries. (d,e) The change in proportion of each resolution path due to differing terminal mispairs was calculated by subtracting the mean proportions for each category of product, first (d)TGCG3′ (3′ G:T) from AGCG3′ (3′ G:A), then (e) 5′GCGT (5′G:T) from 5′GCGA (5′ G:A).
