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. 2012 Feb 22;40(11):5115–5128. doi: 10.1093/nar/gks067

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© The Author(s) 2012. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 8. — Threading intercalation binding mode of 2,7-BisNP (purple) to TT-DNA from NMR-restrained molecular dynamics calculations, viewed (a) from the major groove and (b) from the side of the flipped-out T₁₇. (c) Top view of the naphthalene rings of 2,7-BisNP stacking with the encapsulated thymine T₁₆. (d) Close-up view of the binding site (view from the minor groove, only heteroatom-bound hydrogen atoms are shown) showing direct and water-mediated hydrogen bonds (cyan sticks) between 2,7-BisNP and TT-DNA.