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

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 \({R}_{\text{ee}}\), 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 \(x\approx 0.6L\). 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.

Graphical Abstract

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