Statistical mechanics of base stacking and pairing in DNA melting

TL;DR

This paper introduces a comprehensive statistical mechanics model for DNA melting that explicitly distinguishes base stacking and pairing, validated by experimental data, and highlights the strengths and limitations of existing models.

Contribution

It presents a novel model combining Ising and zipper models for DNA melting, providing a more complete description across all temperatures and experimental validation.

Findings

Ising model accurately describes base stacking transitions.

Experimental data supports the model's validity for stacking.

Limitations identified in the zipper model for base pairing.

Abstract

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 pH 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.