Describing the Structural Diversity within an RNA’s Ensemble

Abstract

RNA is usually classified as either structured or unstructured; however, neither category is adequate in describing the diversity of secondary structures expected in biological systems We describe this diversity within the ensemble of structures by using two different metrics: the average Shannon entropy and the ensemble defect. The average Shannon entropy is a measure of the structural diversity calculated from the base pair probability matrix. The ensemble defect, a tool in identifying optimal sequences for a given structure, is a measure of the average number of structural differences between a target structure and all the structures that make up the ensemble, scaled to the length of the sequence. In this paper, we show examples and discuss various uses of these metrics in both structured and unstructured RNA. By exploring how these two metrics describe RNA as an ensemble of different structures, as would be found in biological systems, it will push the field beyond the standard “structured” and “unstructured” categorization.

Keywords

• secondary structure
• ensemble of structures
• single nucleotide polymorphisms
• ribosome