title: Mesoscopic model for free-energy-landscape analysis of DNA sequences.
abstract: A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter sequences of different organisms. The free energy landscape obtained for these promoters shows a complex structure that is strongly connected to their biological behavior. The analysis method used is able to quantify free energy differences of sites within genome sequences.
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: D
authors.initials: D
authors.lastname: Prada-Gracia
authors.forename: J J
authors.initials: JJ
authors.lastname: Mazo
authors.forename: F
authors.initials: F
authors.lastname: Falo
mesh_terms: D001483:Base Sequence; D003094:Collagen / Q000235:genetics; D004247:DNA / Q000235:genetics*; D000229:Dependovirus / Q000235:genetics; D006801:Humans; D007763:Lac Operon / Q000235:genetics; D008958:Models, Molecular; D025341:Principal Component Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics; D013816:Thermodynamics
chemical_list: D003094:Collagen; D004247:DNA