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 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.
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