title: Classification and predictions of RNA pseudoknots based on topological invariants.
abstract: We propose a new topological characterization of ribonucleic acid (RNA) secondary structures with pseudoknots based on two topological invariants. Starting from the classic arc representation of RNA secondary structures, we consider a model that couples both (i) the topological genus of the graph and (ii) the number of crossing arcs of the corresponding primitive graph. We add a term proportional to these topological invariants to the standard free energy of the RNA molecule, thus obtaining a novel free-energy parametrization that takes into account the abundance of topologies of RNA pseudoknots observed in RNA databases.
authors.affiliation: Department of Physics and Astronomy, Siena College, New York, USA.
authors.forename: Graziano
authors.initials: G
authors.lastname: Vernizzi
authors.affiliation: Institut de Physique Théorique, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.|Beijing Computational Science Research Center, Haidian District Beijing, 100084, China.|Department of Physics, University of California, Santa Barbara, CA 93106, USA.
authors.forename: Henri
authors.initials: H
authors.lastname: Orland
authors.affiliation: Institut de Physique Théorique, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France.|Department of Physics, University of California, Santa Barbara, CA 93106, USA.|Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA.
authors.forename: A
authors.initials: A
authors.lastname: Zee
mesh_terms: D000465:Algorithms; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA