title: Statistical mechanics of base stacking and pairing in DNA melting.
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.
authors.affiliation: Department of Physics and Astronomy, University of California-Los Angeles, Los Angeles, CA 90095-1547, USA.
authors.forename: Vassili
authors.initials: V
authors.lastname: Ivanov
authors.forename: Yan
authors.initials: Y
authors.lastname: Zeng
authors.forename: Giovanni
authors.initials: G
authors.lastname: Zocchi
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D019563:Mechanics; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D013314:Stress, Mechanical; D013696:Temperature
chemical_list: D004247:DNA