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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 6. — Stacking pattern of nucleotides flanking the central triloop motif in the most populated near-native conformational cluster. (Upper panels) Stick representation of nucleotides A5 (green) and G6 (blue) in a representative structure of the folded d(gcGCAgc) hairpin conformational cluster (view along the helical axis of the stem). In case of the cgGCAcg hairpin, the stacking involves C6 (blue) and A5 (green) (lower panels). Stick representation of nucleotides G3 (green) and C2 (blue) in a representative structure of the d(gcGCAgc) hairpin conformational cluster (view along the helical axis of the stem). For the d(cgGCAcg) hairpin the stacking involves G2 (instead of C2).