Statistical mechanics of base stacking and pairing in DNA melting

We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary structure in the whole experimentally accessible temperature range. Base pairing is described through a zipper model, base stacking through an Ising model. We present experimental data on the unstacking transition, obtained exploiting the observation that at moderately low $p\mathrm{H}$ this transition is moved down to experimentally accessible temperatures. These measurements confirm that the Ising model approach is indeed a good description of base stacking. On the other hand, comparison with the experiments points to the limitations of the simple zipper model description of base pairing.

Figure 1

(A1), (B1) Normalized UV absorption spectra $f$ measured at $260\mathrm{nm}$ for the L60 and L36 ds DNA oligomers. The experiments are the circles; the model is the solid line. The data for L36 was fitted using Eqs. (5, 6, 7, 8); for L60 the model was extended to include different pairing interactions for $GC$ and $AT$, as explained in the text. Arrows show the end point of the ds melting transition, determined from the dissociation curves in (A2) and (B2). (A2), (B2) Measured and predicted dissociation curves $p$, for the same oligomers. The measurements were obtained from the quenching method. The model is plotted using the same parameter values as in (A1) and (B1).

Figure 2

Melting curves obtained from UV absorption for the ss oligomers L13 (a) and PH21 (b). Circles are the experimental data; solid lines are the Ising model Eq. (2). The data were obtained at $p\mathrm{H}=3.6$, in order to lower the midpoint of the unstacking transition.

Figure 3

Open circles: normalized UV absorption spectra $f$ measured at $260\mathrm{nm}$ for the L13 (A1) and L13-2 (B) DNA oligomers. The lines are the model. (A2) measured and predicted dissociation curve $p$ for L13. The dashed line in (A2) shows that the dissociation entropy term $\sigma \mathrm{D}$ is needed to account for the $p$ curves. The continuous line in (B) is a fit using the model with ${\sigma }_D=0$ (${\sigma }_D$ is called SD in the figures). The dashed line in (B) shows that the UV spectrum of L13-2 cannot be fitted with the appropriate value ${\sigma }_D=8.0$. This deficiency is due to the oversimplified zipper model description.