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Open Access Publications from the University of California

Effect of secondary structure on the size, configurational statistics, and packaging of long-RNA by viral capsid protein

  • Author(s): Beren, Christian
  • Advisor(s): Gelbart, William M
  • Knobler, Charles M
  • et al.

Many viruses use long (thousands of nucleotides) single-stranded (ss)RNAs as their genomic material. Such viruses can be as simple as a single RNA molecule encapsidated inside a shell (capsid) composed of many copies of a single capsid protein (CP). Cowpea chlorotic mottle virus (CCMV) and brome mosaic virus (BMV), the two sibling viruses studied throughout this work, are model ssRNA viruses that are capable of spontaneous self-assembly \textit{in vitro}. This work aims to elucidate how RNA content affects both the structure of the particles formed and their physical properties. In particular, particles containing one or another of a variety of RNA molecules are compared using physical and biological tools. The results of this work further our understanding of the self-assembly of ssRNA viruses, and the physical forces that result in their structure and dynamical properties.

Chapter one is an introductory chapter, introducing the reader to viruses, ssRNAs and their secondary/tertiary structures, CCMV and BMV, and the \textit{in vitro} self-assembly of these viruses. Chapters two and three discuss the production of viral-length polyU, an RNA molecule that lacks secondary structure due to its inability to base-pair or base-stack, and the packaging of this unique, structureless RNA with CCMV CP. Chapter four discusses the cryo-electron microscopy (cryoEM) asymmetric reconstruction of BMV virions, which allows for unprecedented visualization of the RNA genome inside a multipartite virus--a virus with a genome comprised of more than one RNA packaged into several indistinguishable particles. Chapter five summarizes the results of this work, and provides some future experiments related to the work discussed herein.

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