2004/11/16 by Vassili Ivanov, Yan Zeng, Giovanni Zocchi · 1 citation
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #DNA and Nucleic Acid Chemistry #Protein Structure and Dynamics #RNA and protein synthesis mechanisms #cond-mat.stat-mech #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.1103/physreve.70.051907
published as Phys. Rev. E 70, 051907 (2004) · 13 pages with figures
openalex publication_date 2004/11/16 · arxiv created 2004/11/22 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.