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.