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. 2020 Sep 30;10:16176. doi: 10.1038/s41598-020-73234-6

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Changing the helical phasing between the half sites impacts the kinetic stability and population distribution of p53/DNA complexes. (A) Schematics depicting that in the wild type DNA the half sites are centered on the same face of the DNA helix, insertion of 5 bp between the half sites causes them to be centered on opposite faces of the DNA helix, and insertion of 10 bp results in the half sites being centered on the same face of the DNA helix. (B) Introducing a 5 bp spacer between the two half sites decreases the kinetic stability of one population of p53/DNA complexes. The plot shows bound dwell times from 133 states plotted as a cumulative sums and fit to a double exponential. The 95% confidence intervals for the curve fits are: k_off1 0.03–0.24, k_off2 0.8–1.0. The Y_max values of the curve fit reflect a 27% and 73% distribution between the slow and fast populations, respectively. (C) Increasing the spacing to 10 bp eliminates the more stable population of p53/DNA complexes and alters the kinetic stability of the other population. Shown is a cumulative sums plot of tetramer bound dwell times obtained from replicate experiments. 229 states were fit to a single exponential to obtain the k_off and a 95% confidence interval of 0.47–0.49.