Schematic representations of two chains (I and II) with various possibilities of constraints imposed on the end(s) have been shown. The polygon attached with the end(s) show that the end(s) is (are) constrained by the experimental setup.
Variation of number of intact base pairs and specific heat with temperature for both chains I and II. The peak of specific heat coincides with the value where half of the base pairs are open. Here is scaled by the peak value of C v
(a) Variation of specific heat with temperature for various constraints for chain I. The dotted line, solid line, dashed line, and dotted–dashed line correspond to Figs. 1(a)–1(d), respectively. It is obvious from the plots that peak positions coincides for Figs. 1(b) and 1(c). (b) Same as (a), but for chain II.
The probability profiles of chain I for four different conformations as suggested in Fig. 1. There is a striking difference in the opening of the chain under four different conformations. Figures (a)–(d) correspond to the four conformations as shown in Fig. 1.
For comparison we have plotted the density profile of chain II in one case only. The case when 5′-end of the chain is clamped. In this case two bubbles form, one 2–30, and the other, 50–100. The stronger section of the chain, 31–49 base pairs, resists the opening, which is reflected in the map. In this case the melting temperature can be predicted to be around 345 K.
The probability profile of both the chains under the mechanical stress at 3′ and 5′-ends at T = 300 K. The figure on top left (a) is when chain I is constrained at 3′-end and force is applied at 5′-end, while the figure on top right (b) is for the same chain under reversed conditions. The nature of opening is clearly different in the two cases. While the melting temperature remains unaffected by the way we constrain an end, the force-induced unzipping depends on which end is being constrained. When 3′-end is constrained the opening is sharp, while it is smooth in the reverse case. The last two figures (c) and (d) are for chain II under the same conditions.
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