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Figure 4.
Figure 4. Stretching of nucleosomal DNA. (a) A schematic describing the alignment procedure. Long (turquoise) and
short DNA halves (black and brown, respectively for NCP-PA1,2 and X-NCP) were aligned using LSQMAN (Uppsala
Software Factory). Base-pair 73 is indicated by F. Stretching of the short half occurs at SHL-5 in NCP-PA1 and 2, and at
SHL-2 in X-NCP. Hatched regions indicate those regions of the short half where the sequence is out of register by one
base-pair compared to the long half. (b) Overview of parts of the structure of NCP-PA1, viewed down the superhelical
axis as in Figure 1(a). Only base-pairs 13 -- 78 (short half) and associated proteins are shown. The long half (turquoise,
base-pairs 68 -- 134) was superimposed onto the short half (white) as described for (a). Polyamide 1 is shown in blue;
histone coloring is as described for Figure 1. The dyad axis is indicated by a broken line, base-pair 73 is indicated by
F, the L1L2 DNA-binding motif is indicated by O, the a1 -- a1 motif is indicated by *. (c) X-NCP with aligned long
and short halves (turquoise and gold, respectively) was superimposed onto NCP-PA1 by a structural alignment of 30
base-pairs centered on either stretching site, as shown in (a). All other labels are as in (b).
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