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. Author manuscript; available in PMC: 2013 Mar 14.
Published in final edited form as: J Am Chem Soc. 2012 Feb 27;134(10):4607–4614. doi: 10.1021/ja208466h

Figure 1. Illustration of hairpin folding in the presence or absence of conformational constraint.

Figure 1

PB calculations were performed on ensembles of folded (left) and constrained unfolded (bottom) DNA hairpin structures representing the endpoints of folding in our single-molecule optical trapping assay. Positions of the nucleotides connecting the hairpin to the handles, in the folded hairpin loop, and in the entire unfolded hairpin were randomized by molecular dynamics. See text for explanations of variables.