Effects of the eye phase in DNA unzipping

The onset of the “eye phase” (a phase consisting of configurations of eye-type conformations or bubbles in the double-stranded DNA) and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a “sawtooth” kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.

Figure 1

The schematic of DNA unzipping by force $\left(g\right)$ applied at (a) one end of the two strands; (b) at the interior of the strands, which gives rise to the eye-type conformation. (c)–(e) represent the possible conformations of model C. Here, (c) represents the completely zipped state, (d) a nonpairing configuration, and (e) a partial bound state with a hairpin loop.

Figure 2

Variation of critical force $\left[g_c\left(T\right)\right]$ (END and MID cases) as a function of temperature $\left(T\right)$ for models B and C.

Figure 3

Variation of scaled $⟨m⟩$ (a) with temperature $\left(T\right)$ at constant force $g=0.25$ (END) and 0.50 (MID); (b) with force $\left(g\right)$ at constant $T=0.3$. Here, solid and dashed lines represent the END case, while dot and dotted-dashed line represent the MID case for models B and C, respectively.

Figure 4

Plot of scaled $⟨x⟩$ (a) with force $\left(g\right)$ at constant $T=0.3$ and (b) with temperature $\left(T\right)$ at constant $g=0.25$ (END) and 0.5 (MID). The lines have the same meaning as in Fig. 3.

Figure 5

(a)–(f) represent the $P\left(x\right)$ and $P\left(m\right)$ of the END case (a)–(c) and the MID case (d)–(f) for different forces at constant $T=0.3$. (e) shows the signature of the eye phase of even widths in the form of oscillation for the MID case in model C but is absent in model B.

Figure 6

Schematics showing the different conformations keeping $2x$ ($⩽N^{\nu }$, where $\nu$ is the end-to-end distance exponent) distance constant. For model B, (b) and (c) have the same weight, while for model C, (c) has more weight than (b).

Figure 7

Plot of $⟨g⟩$ with distance $\left(x\right)$ at constant $T=0.5$.