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Role of loop entropy in the force induced melting of DNA hairpin
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Image of FIG. 1.
FIG. 1.

The schematic representations of the ssDNA which can form a hairpin consisting of stem (complementary nucleotides at two ends) and a loop (made up of non-complementary bases). The hairpin fluctuates between the close and open state.

Image of FIG. 2.
FIG. 2.

The schematic representations of transformation of the ssDNA to (a) the dsDNA, (b) a hairpin consisting of a loop and stem, and (c) the extended state. The loop consists of non-complementary nucleotides of the stem.

Image of FIG. 3.
FIG. 3.

Variation of normalized extension(open square) and specific heat (C) (filled circle) with temperature. Solid line corresponds to the sigmoidal fit. (a) for DNA hairpin case (b) for dsDNA case.

Image of FIG. 4.
FIG. 4.

(a) fT diagrams for a DNA hairpin obtained from LD simulations with and without the bending energy term. The arrow indicates the change in the slope which vanishes for k θ = 20; (b) fT diagrams for the dsDNA using LD simulations. The force-temperature diagram is also compared with the FJC and the mFJC models in the reduced unit. Our results are in good agreement with the FJC and the mFJC. The deviation at high force is because of the elastic energy, which is included in the mFJC; (c) and (d) The force-temperature diagrams for the DNA hairpin and the dsDNA using lattice model, which are qualitatively similar to each other. Clear differences between simulation and lattice model are visible at intermediate and high force regime of the force-temperature diagram.

Image of FIG. 5.
FIG. 5.

Temperature-extension curves at different values of the force.

Image of FIG. 6.
FIG. 6.

Variation of extension (up to contour length) with f at T > 0.15. The path retraces and there is no signature of hysteresis; (b) same as (a), but at T < 0.15. Path does not retrace with decreasing f and a force is required to re-zip, which is a signature of hysteresis (dotted and dotted-dashed line) .

Image of FIG. 7.
FIG. 7.

Variation of the applied force with loop length at high and low temperatures.

Image of FIG. 8.
FIG. 8.

(a) Comparison of the probability of opening (P o ) of the stem-end (solid line) and the loop-end (dotted line) with the force for different temperatures. Near the transition point (Fig. 4(a)), the probability of opening is higher for the loop-end; (b) The two probabilities are comparable, and hence, the hairpin can open from both sides; (c) It reflects that opening is always from the stem-end side.


Generic image for table
Table I.

Native matrix elements (A i, j ) of Eq. (1) for two conformational possibilities: a dsDNA and a DNA hairpin.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Role of loop entropy in the force induced melting of DNA hairpin