Strain Softening in Stretched DNA

The microscopic mechanics of DNA stretching was characterized using extensive molecular dynamics simulations. By employing an anisotropic pressure-control method, realistic force-extension dependences of effectively infinite DNA molecules were obtained. A coexistence of $B$ and $S$ DNA domains was observed during the overstretching transition. The simulations revealed that strain softening may occur in the process of stretching torsionally constrained DNA. The latter observation was qualitatively reconciled with available experimental data using a random-field Ising model.

Figure 1

Anisotropic pressure-control simulations of DNA stretching. (a) Setup of MD simulations. The transparent box illustrates the boundaries of the simulated system. Ions are shown as spheres. The DNA outside the transparent box illustrates the periodic boundary condition. (b) Simulated stress-extention dependence. The metastable states are shown as solid symbols with no error bars.

Figure 2

Kinetics of the $B$ to $S$ transition. (a)–(e) The length of a DNA fragment $L_z$ versus simulation time under different values of $P_{zz}$ (sequence $B$), decreasing in steps from $-24$ to $-44\mathrm{bar}$. At $P_{zz}=-34\mathrm{bar}$ (panel c), the gray line corresponds to the last 20-ns fragment of the 40-ns MD trajectory.

Figure 3

(a) Force-extension dependence of a torsionally constrained DNA. Solid symbols indicate the metastable states in the transition region [Fig. 2c]. (b) Force-extension dependence of nicked (circles, triangles) and torsionally constrained (squares) DNA. The inset shows the stable conformation of the torsionally constrained heterogeneous sequence DNA at $L_z/L_0=1.27$. The adenine, thymine, cytosine, and guanine are shown in blue (black), purple (dark gray), orange (gray), and yellow (light gray), respectively.

Figure 4

Phase coexistence during the $B$ to $S$ transition. (a)–(c) Possible conformations of a DNA molecule (sequence $B$) in the elastically stretched (a), transition (b), and overstretched (c) regions under the tensile force of 170 pN. The nucleotides are colored as in Fig. 3b. Panel (c) illustrates a typical conformation of overstretched $S$ DNA, i.e., a partially melted duplex DNA. (d) The average distance between the phosphorous atoms of the DNA backbone (see text) for the DNA conformations shown in (a)–(c).