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

Figure 3.

Figure 3

PFV integration into 601 nucleosomes.A, denaturing PAGE analysis of PFV integration into 601 nucleosomes with a 5′ Cy5 label on the top strand (left, T-Cy5 NPS) or bottom strand (right, B-Cy5 NPS). The DNA size markers are expressed as the nucleosome positions relative to the dyad (–58 to +47 and +58 to –47, respectively). Lane 0 is 601 nucleosome substrate only (NPS). Lanes 1–4 include 7, 13, 20, and 26 nM PFV intasome. Lane 5 is naked 601 NPS DNA only. Lane 6 is naked 601 NPS DNA with 26 nM PFV intasome. B, signal density plots of lane 4 from T-Cy5 NPS (left) and B-Cy5 NPS (right) substrates were generated to quantitate integration activity at integration clusters. C, density plots of lane 4 from T-Cy5 NPS (red) and B-Cy5 NPS (blue) substrates were adjusted to a linear scale and overlaid. The B-Cy5 NPS density plot was slightly shifted to the left to account for the 4 bp between the points of joining. D, integration activity at the four major observed integration clusters over a gradient of PFV intasomes. T-Cy5 NPS (left) and B-Cy5 NPS (right) nucleosome substrates display similar profiles. Error bars indicate the standard deviation between at least three experiments with at least two independent PFV intasome and nucleosome preparations.