Topological classification of RNA structures

Abstract

We present a novel topological classification of RNA secondary structures with pseudoknots. It is based on the topological genus of the circular diagram associated to the RNA base-pair structure. The genus is a positive integer number, whose value quantifies the topological complexity of the folded RNA structure. In such a representation, planar diagrams correspond to pure RNA secondary structures and have zero genus, whereas non planar diagrams correspond to pseudoknotted structures and have higher genus. We analyze real RNA structures from the databases wwPDB and Pseudobase, and classify them according to their topological genus. We compare the results of our statistical survey with existing theoretical and numerical models. We also discuss possible applications of this classification and show how it can be used for identifying new RNA structural motifs.