Fig. 4: Determination of repair intermediates generated when individual human repair factors are omitted.

a cccDNA formation of NA-RrcDNA (lanes 1–6) or RrcDNA (lanes 7–12) by purified human factors was detected by agarose gel electrophoresis containing EtBr. Omission of the factors is indicated by “−”. b Repair products from a were digested with AatII/PsiI and the repair of the plus-strand Pa fragment was monitored by Southern blot as in Fig. 2d. c Repair of the RNA primer-containing Pb fragment was detected by Southern blot as in Fig. 2e. Traces with dashed blue and orange line denote unrepaired (blue arrow head) and repaired (orange arrow head) products of Pb fragments. d–e Repair of minus-strand Ma and Mb fragments were monitored by Southern blot as in Fig. 2f, g. f Removal of the biotin-containing flap of Ma is detected by Streptavidin blot as in Fig. 2h. Rrc, RrcDNA; rL, recombinant linear RrcDNA; ccc, cccDNA. Of note, this figure is related to Supplementary Figure 6, and sections “Omission of individual human factors leads to distinct repair intermediates of the plus-strand” and “Omission of individual human factors leads to distinct repair intermediates of the minus-strand” in the main text. Please refer to these for a comprehensive analysis for the content presented in this figure. All experiments were repeated twice independently. Source data are provided as a Source Data file.