Figure 1

HIV-1 DNA integrates into a DSB site. (A) An experimental procedures for (B)–(D) and (I). Red arrows indicate the primers used in (B) and (D). (B) PCR amplification of WT provirus DNA integrated in the I-SceI site. Each lane depicts each result of twelve samples independently infected with WT virus and Ad-I-SceI (upper panel) or Ad-LacZ (lower panel). M, molecular marker. (C) Upper panel, representative sequencing chromatogram of the PCR amplicon in samples, which were shown in upper panel of (B). Lower panel, summary of viral DNA integration sites. The 18-bp recognition sequence of the I-SceI site is shown. When digested with I-SceI, a 3^′-protruding end of 4 nucleotides is formed (dotted red line). Each arrowhead indicates an actual integration site of viral DNA in samples shown in (B). Integration sites were identified on most of clones except for two clones, which are indicated by arrowheads with a horizontal bar. (D) Effect of KU55933 on viral DNA integration into the I-SceI site. (E) Schematic outline of the I-PpoI-PCR experimental design in (F)–(H) (Top panel). The lentiviral vector was used in this study (bottom panel). (F) PCR amplification of lentiviral vector inserted in the I-PpoI site. Primers are shown by red arrows (G) A representative result of sequence analysis of proviral DNA integrated in the I-PpoI site. (H) Summary of integration sites of the lentiviral vector. Each arrowhead depicts each result of independent clones. The dotted line indicates I-PpoI site with a 3^′-protruding end of 4 nucleotides. (I) Summary of the I-SceI-PCR sequence data. A representative nucleotide sequence was shown at the top of each panel. Asterisks indicate the pAC that would be normally removed during IN-mediated integration (see Additional file 1: Figure S2). Dots indicate identical sequence to that of the representative sequence. Dashes indicate deleted nucleotides.