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. 2019 May 2;10:2063. doi: 10.1038/s41467-019-10026-1

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© The Author(s) 2019

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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Fig. 4 — Molecular basis of REF6 ZnF-clusters and unmethylated DNA. a DNA sequence used for crystal analysis and ITC assay. NAC004P is the partial of NAC004 probe. b Crystal structure of REF6 ZnF2-4 in complex with NAC004 dsDNA. Zinc finger domains are highlighted in blue (ZnF2), lime green (ZnF3), and purple (ZnF4). ZnF2-4 and DNA are shown as cartoon representations. The coding strand of DNA is shown in gray, and the non-coding strand in black. Spheres are Zn atoms. c Structural basis of the interaction of mC₁ with F1339 and D1342. F1339 engages in hydrophobic interactions with 5mC₁ and D1342 forms a weak C–H…O type of hydrogen bond with the 5mC methyl group. d Structural basis of interaction of mC₃ with S1312 and E1315. S1312 makes a weak C–H…O type of hydrogen bond with the 5mC methyl group and E1315 forms a direct H-bond with mC₃. e Modeling a methyl group onto unmodified C₅ in the non-coding strand reveals potential steric hindrance (indicated by a red star) with W1311. f ITC assays showing decreased interaction between REF6-ZnFs and methylated DNA probes. NDB no detectable binding