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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 5. — (A) Hydrogen bonding network formed between C2 (O2′-atom) and A5 (H1N6-atom) as well as two hydrogen bonds formed between G3 and A5 in the sheared base pair geometry in case of the d(gcGCAgc) hairpin. (B) For the d(cgGCAcg) hairpin only the sheared base pair hydrogen bonds are possible (dashed lines). The structures correspond to representative conformations of the most populated conformational cluster (in the lowest temperature replica) of the REMD simulations starting from unfolded single-stranded DNA.