title: A three-state model with loop entropy for the overstretching transition of DNA.
abstract: We introduce a three-state model for a single DNA chain under tension that distinguishes among B-DNA, S-DNA, and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the exponent c in the asymptotic expression S approximately -c ln n for the entropy of a loop of length n. Force extension curves are derived exactly by employing a generalized Poland-Scheraga approach and then compared to experimental data. Simultaneous fitting to force-extension data at room temperature and to the denaturation phase transition at zero force is possible and allows us to establish a global phase diagram in the force-temperature plane. Under a stretching force, the effects of the stacking energy (entering as a domain-wall energy between paired and unpaired bases) and the loop entropy are separated. Therefore, we can estimate the loop exponent c independently from the precise value of the stacking energy. The fitted value for c is small, suggesting that nicks dominate the experimental force extension traces of natural DNA.
authors.affiliation: Physik Department, Technische Universität München, Garching, Germany. einert@ph.tum.de
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Einert
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Staple
authors.forename: Hans-Jürgen
authors.initials: HJ
authors.lastname: Kreuzer
authors.forename: Roland R
authors.initials: RR
authors.lastname: Netz
mesh_terms: D004247:DNA / Q000737:chemistry*; D019277:Entropy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013696:Temperature
chemical_list: D004247:DNA