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. 2017 May 26;7:2466. doi: 10.1038/s41598-017-02397-6

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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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The two- and three-dimensional analysis for a representative pre-miRNA (mir-1301) unedited and edited sequence. (A) The minimum free energy secondary structures and its sequences, colored according to the base-pairing probability. The structure was predicted using RNAFold which uses a loop-based energy model and the dynamic programming algorithm. (B) The corresponding positional entropy for each position. (C) The lowest free energy three-dimensional structure was built using mcfold followed by mcsym where the RNAFold’s secondary structure information was given as structural constrain for unpaired nucleotides. The 5p arm is colored as blue while the 3p arm is colored green, with the edited nucleotide colored as pink. ‘I’ represent the unedited form while ‘II’ represents the edited form. The arrows mark the site of editing. The minimum free energy change at the two- and three dimensional levels for the unedited and edited pre-mirna-1301 is provided in Supplemental Table S5A.