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

Siyu Li, Gonca Erdemci-Tandogan, Paul Van Der Schoot, Roya Zandi

Research output: Contribution to journalArticleAcademicpeer-review

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 an 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.

Original languageEnglish
Article number044002
JournalJournal of Physics Condensed Matter
Volume30
Issue number4
DOIs
Publication statusPublished - 31 Jan 2018

Funding

The authors would like to thank Jef Wagner for useful discussions. This work was supported by the National Science Foundation through Grant No. DMR-1719550 (RZ).

Keywords

  • branched polymer
  • polymer field theory
  • self-assembly
  • virus

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