title: A breathing wormlike chain model on DNA denaturation and bubble: effects of stacking interactions.
abstract: DNA stably exists as a double-stranded structure due to hydrogen-bonding and stacking interactions between bases. The stacking interactions are strengthened when DNA is paired, which results in great enhancement of bending rigidity. We study the effects of this stacking-induced stiffness difference on DNA denaturation and bubble formations. To this end, we model double-stranded DNA as a duplex of two semiflexible chains whose persistence length varies depending on the base-pair distance. Using this model, we perform the Langevin dynamics simulation to examine the characteristics of the denaturation transition and the statistics of the bubbles. We find that the inclusion of the stacking interactions causes the denaturation transition to be much sharper than otherwise. At physiological temperature, the stacking interactions prohibit the initiation of bubble formation but promote bubbles, once grown, to retain the large size.
authors.affiliation: Department of Physics, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea. gazette@postech.ac.kr
authors.forename: Jae-Yeol
authors.initials: JY
authors.lastname: Kim
authors.forename: Jae-Hyung
authors.initials: JH
authors.lastname: Jeon
authors.forename: Wokyung
authors.initials: W
authors.lastname: Sung
mesh_terms: D001482:Base Composition; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation
chemical_list: D004247:DNA