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 3. (a) The bending energy ΔEbend(θ) versus bending angle θ over the central 14 base pairs, for AA-TT, AT-TA and GENE. (b) The electrostatic bending energy ΔEel(θ) versus bending angle θ over the central 14 base pairs for AA-TT, AT-TA and GENE. Here, ΔEel(θ) was calculated directly with the APBS [68]. (c) The non-electrostatic bending energy ΔEnel(θ) versus bending angle θ over the central 14 base pairs for AA-TT, AT-TA and GENE. The electrostatic energies and the surface potentials in panels (b), (c) were calculated with the APBS [68].