Coarse-Grained Molecular Dynamics Model of Double-Stranded DNA for DNA Nanostructure Design

A new coarse-grained molecular dynamics double-stranded DNA model (nCG-dsDNA model) using an improved beads-spring model was proposed. In this model, nucleotide comprising phosphate, sugar, and base group were replaced by a single bead. The double stranded model with 202 base pairs was created to tune the parameters of the bond, the nonbond, stack, angle bending, and electrostatic interaction. The average twisted angle and the persistence length of the model without electrostatic interaction were calculated at 35.3° and 120.3 bp, confirming that the proposed model successfully realized the experimentally observed double-stranded DNA structure. Moreover, the model with electrostatic interaction was discussed. From calculation results, we confirmed that the dependency of the salt concentration on the persistence length of the nCG-dsDNA model at the 30% charge is in good agreement with the Poisson-Boltzmann theoretical model.