Probing Viral Genomic Structure: Alternative Viewpoints and Alternative Structures for Satellite Tobacco Mosaic Virus RNA

Turner

2014

Nucleic Acids Research

154

124

Oligonucleotide microarrays are widely used in various biological studies. In this review, application of oligonucleotide microarrays for identifying binding sites and probing structure of RNAs is described. Deep sequencing allows fast determination of DNA and RNA sequence. High-throughput methods for determination of secondary structures of RNAs have also been developed. Those methods, however, do not reveal binding sites for oligonucleotides. In contrast, microarrays directly determine binding sites while also providing structural insights. Microarray mapping can be used over a wide range of experimental conditions, including temperature, pH, various cations at different concentrations and the presence of other molecules. Moreover, it is possible to make universal microarrays suitable for investigations of many different RNAs, and readout of results is rapid. Thus, microarrays are used to provide insight into oligonucleotide sequences potentially able to interfere with biological function. Better understanding of structure–function relationships of RNA can be facilitated by using microarrays to find RNA regions capable to bind oligonucleotides. That information is extremely important to design optimal sequences for antisense oligonucleotides and siRNA because both bind to single-stranded regions of target RNAs.

Section: Future Improvements and Potentialmentioning

confidence: 99%

Microarrays for identifying binding sites and probing structure of RNAs

Turner

2014

Nucleic Acids Research

154

124

“…11 In contrast, multiple models have been proposed for the conformation of the in virio RNA that have emphasized short helices, without long-range base-pairing interactions, based on computational-only secondary structure modeling. 2,4,9,12-14 These models vary significantly, reflecting, in part, the difficulty in modeling the secondary structure of a large RNA when extensive protein-RNA interactions are present. 9 Here we combine results of several recently developed chemical probing strategies to overcome previous limitations and develop a well-defined model for the secondary structure of the STMV RNA genome as it exists inside authentic virions and in the absence of the capsid.…”

Section: Introductionmentioning

confidence: 99%

Packaged and Free Satellite Tobacco Mosaic Virus (STMV) RNA Genomes Adopt Distinct Conformational States

2017

The RNA genomes of viruses likely undergo multiple functionally important conformational changes during their replication cycles, changes that are poorly understood at present. We used two complementary in-solution RNA structure probing strategies (SHAPE-MaP and RING-MaP) to examine the structure of the RNA genome of satellite tobacco mosaic virus inside authentic virions and in a capsid-free state. Both RNA states feature similar three-domain architectures in which each major replicative function – translation, capsid coding, and genome synthesis – fall into distinct domains. There are, however, large conformational differences between the in-virion and capsid-free states, primarily in one arm of the central T domain. These data support a model in which the packaged capsid-bound RNA is constrained in a local high-energy conformation by the native capsid shell. The removal of the viral capsid then allows the RNA genome to relax into a more thermodynamically stable conformation. These data support a model in which the RNA architecture of the central T domain changes during capsid assembly and disassembly and may play a role in genome packaging.

“…If the charge density of the capsid is high, the genome mostly sits close to the wall, otherwise, due to entropic effects for the low capsid charge density, the RNA concentration is higher at the center of the capsid [39]. [13,14,17] respectively. Their relative sizes are not at scale.…”

mentioning

confidence: 99%

RNA Base Pairing Determines the Conformations of RNA Inside Spherical Viruses

2017

Many simple RNA viruses enclose their genetic material by a protein shell called the capsid. While the capsid structures are well characterized for most viruses, the structure of RNA inside the shells and the factors contributing to it remain poorly understood. We study the impact of base pairing on the conformations of RNA and find that it undergoes a swollen coil to globule continuous transition as a function of the strength of the pairing interaction. We also observe a first order transition and kink profile as a function of RNA length. All these transitions could explain the different RNA profiles observed inside viral shells.