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Mechanistic mapping of temperature-dependent ssDNA elasticity with oxDNA2 coarse-grained model.

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Title: Mechanistic mapping of temperature-dependent ssDNA elasticity with oxDNA2 coarse-grained model.
Authors: Igwe, Isaiah Eze1 (AUTHOR) iigwe@fudutsinma.edu.ng, Abdulfatah, Saratu1,2 (AUTHOR)
Source: European Physical Journal E -- Soft Matter. Apr2026, Vol. 49 Issue 4, p1-18. 18p.
Subjects: Single-stranded DNA, Stacking interactions, Temperature effect
Abstract: The mechanical behavior of single-stranded DNA (ssDNA) controls its biological function and underpins the design of DNA-based nanodevices, yet the microscopic origin of temperature-dependent elasticity remains incompletely quantified. Here, we use the salt-aware, sequence-dependent oxDNA2 coarse-grained model to map how intra-strand stacking and temperature jointly determine ssDNA mechanics for two prototypical homopolymers, poly(dA)50 and poly(dT)50, across 27–100 °C at 1.0 M monovalent salt. Large ensembles of independent simulations were used to extract equilibrium observables such as persistence length l p , radius of gyration R g , end-to-end distance R ee , and equilibrium force–extension relations. We find that poly(dA) is substantially stiffer than poly(dT) at low temperature: l p ​ = 44.8 ± 2.0 nm at 27 °C decreases to 10.0 ± 0.7 nm at 100 °C, while poly(dT) remains comparatively flexible, varying only from 1.40 ± 0.08 nm to 1.05 ± 0.04 nm. These macroscopic changes closely track the loss of intra-strand stacking. For poly(dA), the stacking fraction decreases from 0.70 ± 0.02 to 0.20 ± 0.01, whereas poly(dT) remains weakly stacked across the full range (< 0.10). Force–extension analysis shows that the wormlike chain (WLC) model captures low-force entropic elasticity but fails at intermediate extensions in strongly stacked poly(dA), where cooperative unstacking produces excess forces of ~ 8 to 10 pN near x ≈ 0.6 L . The normalized root-mean-square residual at 27 °C is 0.22 for poly(dA), compared to 0.03 for poly(dT). When l p is normalized by its 27 °C value, both sequences collapse onto a single master curve as a function of stacking fraction (collapse slope ≈ 3.5 ± 0.3), indicating that fractional stacking loss serves as a unifying control parameter for thermal softening. These results quantitatively link microscopic stacking statistics to macroscopic elasticity, clarify the temperature-dependent limits of continuum polymer models, and provide a mechanistic framework for interpreting single-molecule stretching and ensemble measurements of ssDNA mechanics. [ABSTRACT FROM AUTHOR]
Copyright of European Physical Journal E -- Soft Matter is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Mechanistic mapping of temperature-dependent ssDNA elasticity with oxDNA2 coarse-grained model.
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  Data: &lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Igwe%2C+Isaiah+Eze%22&quot;&gt;Igwe, Isaiah Eze&lt;/searchLink&gt;&lt;relatesTo&gt;1&lt;/relatesTo&gt; (AUTHOR)&lt;i&gt; iigwe@fudutsinma.edu.ng&lt;/i&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;AR&quot; term=&quot;%22Abdulfatah%2C+Saratu%22&quot;&gt;Abdulfatah, Saratu&lt;/searchLink&gt;&lt;relatesTo&gt;1,2&lt;/relatesTo&gt; (AUTHOR)
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  Data: &lt;searchLink fieldCode=&quot;JN&quot; term=&quot;%22European+Physical+Journal+E+--+Soft+Matter%22&quot;&gt;European Physical Journal E -- Soft Matter&lt;/searchLink&gt;. Apr2026, Vol. 49 Issue 4, p1-18. 18p.
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  Data: &lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Single-stranded+DNA%22&quot;&gt;Single-stranded DNA&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Stacking+interactions%22&quot;&gt;Stacking interactions&lt;/searchLink&gt;&lt;br /&gt;&lt;searchLink fieldCode=&quot;DE&quot; term=&quot;%22Temperature+effect%22&quot;&gt;Temperature effect&lt;/searchLink&gt;
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: The mechanical behavior of single-stranded DNA (ssDNA) controls its biological function and underpins the design of DNA-based nanodevices, yet the microscopic origin of temperature-dependent elasticity remains incompletely quantified. Here, we use the salt-aware, sequence-dependent oxDNA2 coarse-grained model to map how intra-strand stacking and temperature jointly determine ssDNA mechanics for two prototypical homopolymers, poly(dA)50 and poly(dT)50, across 27–100 &#176;C at 1.0 M monovalent salt. Large ensembles of independent simulations were used to extract equilibrium observables such as persistence length l p , radius of gyration R g , end-to-end distance R ee , and equilibrium force–extension relations. We find that poly(dA) is substantially stiffer than poly(dT) at low temperature: l p ​ = 44.8 &#177; 2.0 nm at 27 &#176;C decreases to 10.0 &#177; 0.7 nm at 100 &#176;C, while poly(dT) remains comparatively flexible, varying only from 1.40 &#177; 0.08 nm to 1.05 &#177; 0.04 nm. These macroscopic changes closely track the loss of intra-strand stacking. For poly(dA), the stacking fraction decreases from 0.70 &#177; 0.02 to 0.20 &#177; 0.01, whereas poly(dT) remains weakly stacked across the full range (&lt; 0.10). Force–extension analysis shows that the wormlike chain (WLC) model captures low-force entropic elasticity but fails at intermediate extensions in strongly stacked poly(dA), where cooperative unstacking produces excess forces of ~ 8 to 10 pN near x ≈ 0.6 L . The normalized root-mean-square residual at 27 &#176;C is 0.22 for poly(dA), compared to 0.03 for poly(dT). When l p is normalized by its 27 &#176;C value, both sequences collapse onto a single master curve as a function of stacking fraction (collapse slope ≈ 3.5 &#177; 0.3), indicating that fractional stacking loss serves as a unifying control parameter for thermal softening. These results quantitatively link microscopic stacking statistics to macroscopic elasticity, clarify the temperature-dependent limits of continuum polymer models, and provide a mechanistic framework for interpreting single-molecule stretching and ensemble measurements of ssDNA mechanics. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: &lt;i&gt;Copyright of European Physical Journal E -- Soft Matter is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder&#39;s express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.&lt;/i&gt; (Copyright applies to all Abstracts.)
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        Value: 10.1140/epje/s10189-026-00578-8
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      – Code: eng
        Text: English
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        PageCount: 18
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    Subjects:
      – SubjectFull: Single-stranded DNA
        Type: general
      – SubjectFull: Stacking interactions
        Type: general
      – SubjectFull: Temperature effect
        Type: general
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      – TitleFull: Mechanistic mapping of temperature-dependent ssDNA elasticity with oxDNA2 coarse-grained model.
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            NameFull: Igwe, Isaiah Eze
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            NameFull: Abdulfatah, Saratu
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            – D: 01
              M: 04
              Text: Apr2026
              Type: published
              Y: 2026
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