title: Statistics of topological RNA structures.
abstract: In this paper we study properties of topological RNA structures, i.e. RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological structures having genus zero. We derive a new bivariate generating function whose singular expansion allows us to analyze the distributions of arcs, stacks, hairpin- , interior- and multi-loops. We then extend this analysis to H-type pseudoknots, kissing hairpins as well as 3-knots and compute their respective expectation values. Finally we discuss our results and put them into context with data obtained by uniform sampling structures of fixed genus.
authors.affiliation: Biocomplexity Institute of Virginia Tech, Blacksburg, VA, 24061, USA.
authors.forename: Thomas J X
authors.initials: TJX
authors.lastname: Li
authors.affiliation: Biocomplexity Institute of Virginia Tech, Blacksburg, VA, 24061, USA. duckcr@vbi.vt.edu.
authors.forename: Christian M
authors.initials: CM
authors.lastname: Reidys
mesh_terms: D000465:Algorithms; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*
chemical_list: D012313:RNA
keywords: Fatgraph; Generating function; Genus; Loop; Pseudoknot; RNA structure; Singularity analysis