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. 2021 Jun 17;8:693710. doi: 10.3389/fmolb.2021.693710

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Copyright © 2021 Sengar, Ouldridge, Henrich, Rovigatti and Šulc.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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The response of ssDNA to tension, and the role of stacking therein. (A) Force-extension plots for 100-nucleotide poly (dA) using three models: no stacking (black); average stacking strength (oxDNA1.0, blue) and sequence-dependent stacking (oxDNA1.5, red). Stronger stacking leads to an increased force at larger extensions, and extremely strong stacking results in a plateau-like feature as stacking is disrupted. (B) Stacking probability for average stacking strength (oxDNA1.0, blue) and sequence-dependent stacking (oxDNA1.5, red) as a function of applied force. Adjacent nucleotides are defined as stacked if the stacking energy between the pair is more than -0.1 units.