To develop our coarse-grained model of ssDNA, we first performed an all-atom reference simulation of dT60 using current best practices for simulations involving DNA–ion interactions. The all-atom trajectory was mapped into a coarse-grained representation featuring two beads per nucleotide. Distributions of bonds, angles and dihedral angles as well as non-bonded pair distribution functions were extracted from the coarse-grained reference trajectory. Using iterative Boltzmann inversion, coarse-grained potentials were iteratively tuned until simultations produced distributions that closely matched the reference distributions.
After the coarse-grained potentials were refined to reproduce distributions extracted from all-atom simulation, the coarse-grained ssDNA was found to have a smaller radius of gyration (a measure of size) than expected from experiment. We added a small amount of Yukawa repulsion between non-bonded P beads until the radius of gyration for a 60-nucleotide fragment matched experimental measurements. No further adjustements were made to the model.