Figure 2.

Exploring the effects predicted by model 1. Plots for the length of the looped section, L_loop and the extension length, z (defined in figure 1), as a function of applied force, for various values of the model parameters, calculated using equations (3.1), (3.2) and (3.4). Here, the typical value of b=2l_p= 1000 Åis used. Plots of L_loop, normalized over $L_{max}\approx 34\hspace{0.17em}000$ Å(the maximum length for pairing of the homologous segments) are shown in (a,b). Plots of z divided by the total DNA length L are shown in (c,d). Here, the thin solid line is the extension–force curve, which would have emerged for total homologous pairing ($L_{\mathrm{loop}}=L_{max}$); the thin dotted line is that for no pairing (L_loop=0). The insets in (c,d) show Δz, the difference in extension between the case with no pairing (thin dotted line) and those with homologous pairing. In (a,c), ε_loop=0.5 k_BT/ Å, and the thick solid, long dashed, medium dashed and short dashed lines correspond to the values a=200, 150, 100, 70 k_BT/ Å^1/2. In (b,d), a=100 k_BT/ Å^1/2, and the solid, long dashed, medium dashed and short dashed lines correspond to the values ε_loop=0.1,0.2,0.4,0.8 k_BT/ Å. (Online version in colour.)