Topological classification of RNA structures.
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. The topological genus allows for the definition of topological folding motifs, similar in spirit to those introduced and commonly used in protein folding. We analyze real RNA structures from the databases Worldwide Protein Data Bank and Pseudobase and classify them according to their topological genus. For simplicity, we limit our analysis by considering only Watson-Crick complementary base pairs and G-U wobble base pairs. 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.
Bon
Michael
M
Service de Physique Théorique, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France; Ecole Nationale Supérieure des Mines de Paris, 75006 Paris, France.
Vernizzi
Graziano
G
Orland
Henri
H
Zee
A
A
D020029:Base Pairing; D001483:Base Sequence; D030561:Databases, Nucleic Acid; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D012329:RNA, Bacterial / Q000737:chemistry / Q000145:classification / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000737:chemistry / Q000145:classification / Q000235:genetics
D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; D012313:RNA