Coarse-grained modeling on sequence-dependent 3D structure size of single-stranded DNA in ion solutions

We have developed a DNA coarse-grained (CG) model, which can make reliable predictions on 3D structures and stability for both double-stranded (dsDNA) and single-stranded (ssDNA) DNAs from their sequences. However, the CG model cannot capture the effect of base variations in single-stranded regions on the 3D structure. In this work, we further developed the CG model by including the sequence-dependent single-stranded base-stacking interactions to predict the conformations of ssDNAs with homogeneous sequence. Testing on poly-A and poly-T with different lengths (8-120nt) has shown that the present model can successfully reproduce the experimentally measured sequence-dependent structural size of ssDNA. Furthermore, the present model can also accurately predict the salt-dependences of structural sizes and Flory scaling exponents for both poly-A and poly-T with a wide range of ion concentrations $\left(10 \mathrm{mM}-1025 \mathrm{mM}\left[\mathrm{Na}^{+}\right]\right)$. Additionally, the model also captures the observation that poly-A exhibits a weaker dependence on ion concentration compared to poly-T due to its stronger base-stacking interactions. The developed model is freely available on GitHub: https://github.com/RNA-folding-lab/DNAfold.