title: Thermal and mechanical properties of a DNA model with solvation barrier.
abstract: We study the thermal and mechanical behaviors of DNA denaturation in the frame of the mesoscopic Peyrard-Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we are able to set suitable values of the parameters of the model and study the formation and stability of bubbles in the system. Then, we focus on the case of the P5 promoter sequence and use the principal component analysis of the trajectories to extract the main information on the dynamical behavior of the system. We find that this analysis method gives an excellent agreement with previous biological results.
authors.affiliation: Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain.
authors.forename: R
authors.initials: R
authors.lastname: Tapia-Rojo
authors.forename: J J
authors.initials: JJ
authors.lastname: Mazo
authors.forename: F
authors.initials: F
authors.lastname: Falo
mesh_terms: D001483:Base Sequence; D001696:Biomechanical Phenomena; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D055595:Mechanical Phenomena; D008954:Models, Biological; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D025341:Principal Component Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D012997:Solvents / Q000737:chemistry*; D044366:Transition Temperature
chemical_list: D012333:RNA, Messenger; D012997:Solvents; D004247:DNA