The effect of RNA stiffness on the self-assembly of virus particles

TL;DR

This study investigates how RNA stiffness, influenced by base-pairing, affects the efficiency of viral genome encapsidation, revealing that increased stiffness can favor linear over branched RNA in packaging.

Contribution

It introduces a model linking RNA stiffness due to base-pairing with encapsidation free energy, explaining the preference for linear RNA in viral packaging.

Findings

Increased RNA stiffness can reduce encapsidation efficiency.

Branching makes RNA more compact, aiding packaging.

Base-pairing increases effective chain length, impacting free energy.

Abstract

Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be compact and highly branched because of long distance base-pairing between nucleotides, recent experiments reveal that in a head-to-head competition between a ssRNA with no secondary or higher order structure and a viral RNA, the capsid proteins preferentially encapsulate the linear polymer! In this paper, we study the impact of genome stiffness on the encapsidation free energy of the complex of RNA and capsid proteins. We show that an increase in effective chain stiffness because of base-pairing could be the reason why under certain conditions linear chains have an advantage over branched chains when it comes to encapsidation efficiency. While branching makes the genome more compact, RNA base-pairing increases the effective Kuhn length of the RNA molecule, which could result in an increase of the free energy of RNA confinement, that is, the work required to encapsidate RNA, and thus less efficient packaging.