title: DNA loci cross-talk through thermodynamics.
abstract: The recognition and pairing of specific DNA loci, though crucial for a plenty of important cellular processes, are produced by still mysterious physical mechanisms. We propose the first quantitative model from Statistical Mechanics, able to clarify the interaction allowing such "DNA cross-talk" events. Soluble molecules, which bind some DNA recognition sequences, produce an effective attraction between distant DNA loci; if their affinity, their concentration, and the relative DNA binding sites number exceed given thresholds, DNA colocalization occurs as a result of a thermodynamic phase transition. In this paper, after a concise report on some of the most recent experimental results, we introduce our model and carry out a detailed "in silico" analysis of it, by means of Monte Carlo simulations. Our studies, while rationalize several experimental observations, result in very interesting and testable predictions.
authors.affiliation: Dipartimento di Scienze Fisiche, Università di Napoli "Federico II", 80126 Napoli, Italy. antonio.scialdone@na.infn.it
authors.forename: Antonio
authors.initials: A
authors.lastname: Scialdone
authors.forename: Mario
authors.initials: M
authors.lastname: Nicodemi
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry / Q000235:genetics; D022004:Chromosome Structures; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D056426:Genetic Loci; D008957:Models, Genetic; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D015398:Signal Transduction; D013816:Thermodynamics; D049951:X Chromosome Inactivation
chemical_list: D002843:Chromatin; D004247:DNA