New coarse-grained molecular dynamics model of double stranded DNA chain for DNA origami

Abstract

New coarse-grained molecular dynamics model of double stranded DNA (nCG-dsDNA model) was reported. The nCG-dsDNA model was made by newly developed simple bead-spring model for realizing a helix structure. The phosphate group, sugar group, and base group in an actual double stranded DNA chain were represented by a single bead. The nCG-dsDNA model with 202 base pair was utilized to tune the bond potential between connected two beads of a chain, the nonbond potential between stack sites and the angle bending potential between three beads. The twisted angle of each chains in the model was calculated as 35.3 degree. From this result, it was confirmed that the actual double stranded DNA structure was well realized by the proposed model. Moreover, it was confirmed that a persistence length of the nCG-dsDNA model was in good agreement with the results of conventional DNA model (oxDNA model) and experiments.