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. 2013 Aug 16;41(21):9881–9890. doi: 10.1093/nar/gkt739

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© The Author(s) 2013. Published by Oxford University Press.

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

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Figure 2. — Effect of ionic strength on duplex DNA bending in molecular vises. (A) FRET efficiency as a function of target strand length for five loop sizes (colors as in Figure 1C). Addition of 50 mM NaCl did not shift the buckling transition from its original position at 40 bp (left). The presence of 250 mM NaCl (center) or of 50 mM NaCl and 1 mM MgCl₂ (right) led to a new bending transition at a target strand length of 30 bp and a loss of contrast in the original buckling transition at 40 bp. The transition at 30 bp is inconsistent with Euler buckling and represents a physically distinct bending mode, which we term ‘kinking’. (B) The transition of the dominant bending mode from Euler buckling to kinking was quantified by (as indicated in A). In a background of 89 mM tris/borate, the transition occurred between 50 and 100 mM NaCl (left). In 89 mM tris/borate and 50 mM NaCl, the transition occurred on addition of 1 mM MgCl₂ (right), indicating that Mg²⁺ stabilized the kinked structure significantly more efficiently than did Na⁺. Full FRET curves for all ionic conditions are in Supplementary Figure S2. Error bars are SEM from at least three independent replicates.

Inline graphic — Effect of ionic strength on duplex DNA bending in molecular vises. (A) FRET efficiency as a function of target strand length for five loop sizes (colors as in Figure 1C). Addition of 50 mM NaCl did not shift the buckling transition from its original position at 40 bp (left). The presence of 250 mM NaCl (center) or of 50 mM NaCl and 1 mM MgCl₂ (right) led to a new bending transition at a target strand length of 30 bp and a loss of contrast in the original buckling transition at 40 bp. The transition at 30 bp is inconsistent with Euler buckling and represents a physically distinct bending mode, which we term ‘kinking’. (B) The transition of the dominant bending mode from Euler buckling to kinking was quantified by (as indicated in A). In a background of 89 mM tris/borate, the transition occurred between 50 and 100 mM NaCl (left). In 89 mM tris/borate and 50 mM NaCl, the transition occurred on addition of 1 mM MgCl₂ (right), indicating that Mg²⁺ stabilized the kinked structure significantly more efficiently than did Na⁺. Full FRET curves for all ionic conditions are in Supplementary Figure S2. Error bars are SEM from at least three independent replicates.