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. 2017 Apr 26;7:1178. doi: 10.1038/s41598-017-01348-5

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© The Author(s) 2017

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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Initial configuration of the MD simulation of the predicted 3D ssDNA structure for the sequence CGCGGTGTCCGCG, corresponding to 1LA8. Only the molecules within the central simulation cell are shown. The ssDNA molecule was solvated in water and the system charge neutralized with 12 sodium ions. The atoms of the water molecules are represented as white (hydrogen) and red (oxygen) lines and the sodium ions are displayed as yellow spheres with radii corresponding to its atomic van der Waals radius. The ssDNA molecule is shown in blue with the backbone and bases represented as new ribbons and the additional components represented as lines. The unit cell dimensions are L _x = 72 Å, L _y = 72 Å, and L _z = 78 Å.