Figure 4: Bending energy distribution of dsDNA.
(a) dsDNA conformation was obtained by fitting the standard dsDNA model into the IPET 3D density map. (b) Schematic model illustrating that the nanogold interacts with the dsDNA and that the dsDNA contains kink regions that carry bending elasticity. (c) Cylinder model illustrating the bending angles between two connected base pairs. The cylinder is defined by the two consecutive dsDNA base pairs. (d) The bending angle can be presented by the angle θi, formed by the centres of three consecutive cylinders, or (e) by the angle ϕi, formed by the centre axes of two consecutive cylinders. (f) Based on the two types of measured angles, θi and ϕi, the bending energies for each DNA conformation were calculated and plotted based on a simple WLC model. The averaged bending energies from the two types of angles are indicated by the dashed lines. The bending energy of the standard DNA model was also calculated and indicated as structure no. 0 as a control.
