Viral RNA as a branched polymer

TL;DR

This paper explores the physical structure of viral RNA, modeling it as a branched polymer to understand its compactness and properties, and relates this to experimental and computational approaches in RNA folding.

Contribution

It introduces a novel approach of treating viral RNA as branched polymers using planar graphs, linking polymer physics to RNA structure analysis.

Findings

Viral RNA genomes exhibit characteristic compactness distinct from random RNAs.

RNA folding software parameters influence structural predictions and observable properties.

The branched polymer model can incorporate additional interactions like electrostatics.

Abstract

Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a repository of genetic material, viral RNA performs numerous other functions mediated by its physical structure and chemical properties. In this chapter, we focus on its structure and discuss how long RNA molecules can be treated as branched polymers through planar graphs. We describe the major results that can be obtained by this approach, in particular the observation that viral RNA genomes have a characteristic compactness that sets them aside from similar random RNAs. We also discuss how different parameters used in the current RNA folding software influence the resulting structures and how they can be related to experimentally observable quantities. Finally, we show how the connection to branched polymers can be extended to take advantage of known results from polymer physics and can be further moulded to include additional interactions, such as excluded volume or electrostatics.