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. 2011 Jun 30;39(19):8271–8280. doi: 10.1093/nar/gkr541

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© The Author(s) 2011. 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 7. — Calculated free energy change (PMF) obtained from US simulations along the distance of the terminal phosphate groups starting from folded hairpin conformations. The upper panels show a superposition of sampled intermediate conformations [left panel: d(gcGCAgc) and right panel: d(cgGCAcg)] obtained from the US window at 20.5 Å phosphate–phosphate distance. Nucleotides are shown in blue except for G3 and A5 (atom color code). In case of the gcGCAgc sequence the sheared G3:A5 arrangement is frequently preserved, whereas in case of the cgGCAcg, it is largely replaced by a G3:A5 contact similar to the structure observed in the second most populated cluster from the REMD of the d(cgGCAcg) hairpin.