Understanding sequence effect in DNA bending elasticity by molecular dynamic simulations

Xiao-Wei Qiang,Hai-Long Dong,Kai-Xin Xiong,Wenbing Zhang,Zhi-Jie Tan

Figure 5. (a) A grooved coarse-grained model for DNA structure [71, 72], where every base pair is composed of two phosphate spheres (in red), two sugar spheres (in blue) and one big base sphere (in yellow); see details in the appendix. (b) The electrostatic energy for straight 14-bp DNAs (bending angle θ = 0) with different minor groove widths from the grooved DNA model. (c) The electrostatic bending energy ΔEel(θ) for a 14-bp DNA versus bending angle θ over central 6 base pairs. The electrostatic energies and the surface potentials in panels (b), (c) were calculated with the APBS [68].