Eur. Phys. J. E (2026) 49: 35
https://doi.org/10.1140/epje/s10189-026-00578-8

Research - Living Systems

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

¹ Department of Physics, Federal University Dutsin-Ma, 821101, Katsina State, Nigeria
² Department of Physics, Umaru Musa Yar’dua University Batagarawa, 820102, Katsina State, Nigeria

^a This email address is being protected from spambots. You need JavaScript enabled to view it.

Received: 5 January 2026
Accepted: 17 March 2026
Published online: 12 April 2026

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.