Fig. 3
a Sketch of the original simulations performed in this work where we consider a segment of DNA 1.6 kbp long (or N=200 beads, each bead representing 8 bp) with rigidity lp=150 bp. The DNA is interspersed with “soft” sites which display a different rigidity lf. The length of these weak sites is 8 bp, or 1 bead. b We compute the frequency of integration events per each segment of the substrate by counting the number of events occurring at a specific locus over the total integration events. We average over 1000 independent simulations. One can notice that the patterns, which are roughly uniform for lf=lp become more and more periodic and reflecting the positions of the soft sites (denoted by the black arrows) when we reduce lf. The dotted line shows the expected frequency for random events 1/N, with N=200 the length of the substrate. For clarity we report only the segment 0.5–1 kbp. c Integration enhancement in soft sites over the expected random frequency. Each box represents a different value of the rigidity of the soft sites lf. Recall that lf=lp=150 bp reflects a uniformly stiff substrate and indeed we recover the expected value (unity) for the enhancement