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. 2020 Feb 7;10:2079. doi: 10.1038/s41598-019-55660-3

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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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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The contour map generated from our LWPH based PCA models for DNA configurations in IL and WAT environments. The x-axis and y-axis are the first and second principal components. (a₁) The DNA configuration ensemble for all three trajectories for IL. (a₂–a₄) Three DNA configuration trajectories from the MD simulation with IL. (b₁) The DNA configuration ensemble for all three trajectories in water environment. (b₂–b₄) Three DNA configuration trajectories from the MD simulation using water solution. It can be seen clearly that areas of contour map in IL are much smaller than in water, indicating the confinement effect of the DNA configurations in IL. Further, contour graph for IL1 (a₂) shows a clear difference of that for IL2 (a₃) and IL3 (a₄), meaning there is a subtle change of the ion-DNA binding mode in trajectory IL1.