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. 2021 Mar 18;296:100550. doi: 10.1016/j.jbc.2021.100550

Figure 1.

Figure 1

PFV integration into a linear DNA target.A, illustration of PFV concerted integration to 601 NPS DNA, not drawn to scale. PFV 40 bp vDNA (thin lines) in the context of an intasome is added to 601 NPS DNA (thick lines) wrapped around a histone octamer. The 601 NPS is 147 bp numbered –73 to +73 with 0 at the central dyad. Integration of the vDNA to the NPS yields an integration intermediate. The two PFV strand transfer events are separated by 4 bp of target DNA, indicated by numbers 0–3. For a single concerted integration, two integration products are formed. When analyzed by native gel electrophoresis, the products appear as two bands. Each product is one vDNA, a fraction of the NPS DNA, and a four base gap. Black circles indicate 5′ ends. B and C, the NPS DNA may be fluorescently labeled (red or blue diamond) on either the top (T-Cy5 NPS) or bottom (B-Cy5 NPS) strand. The integration strand transfers introduce nicks in the target DNA. Each nick is immediately adjacent to a point of joining. Denaturing gel electrophoresis isolates the NPS DNA fragment that is not joined to the vDNA. As an example, concerted integration could yield a 37 nt fragment and a 106 nt fragment (37 nt + 106 nt + 4 nt space between strand transfers = 147 nt, the length of 601). Based on the 601 numbering, the vDNA is joined to T-Cy5 NPS DNA at –36 and B-Cy5 NPS -33. Integration position 0 is at 601 NPS position –36.