ArticlePloS one2013
In vitro secondary structure of the genomic RNA of satellite tobacco mosaic virus.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 27 citations in OpenAlex.
- Article
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- Viral RNA structure analysis using DMS-MaPseq.Methods (San Diego, Calif.) · 2020Review
- Physical and Functional Analysis of Viral RNA Genomes by SHAPE.Annual review of virology · 2019Review
- Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.Nucleic acids research · 2018Article
- Packaged and Free Satellite Tobacco Mosaic Virus (STMV) RNA Genomes Adopt Distinct Conformational States.Biochemistry · 2017Article
- Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures.Biophysical journal · 2016Article
- Viral RNA switch mediates the dynamic control of flavivirus replicase recruitment by genome cyclization.eLife · 2016Article
- Biologically-supported structural model for a viral satellite RNA.Nucleic acids research · 2015Article
- The Role of Packaging Sites in Efficient and Specific Virus Assembly.Journal of molecular biology · 2015Article
- Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy.RNA (New York, N.Y.) · 2015Article
- Mechanisms of virus assembly.Annual review of physical chemistry · 2015Review
- Native Purification and Analysis of Long RNAs.Methods in enzymology · 2015Article
- Functional long-range RNA-RNA interactions in positive-strand RNA viruses.Nature reviews. Microbiology · 2014Review
- Long-range architecture in a viral RNA genome.Biochemistry · 2013Article
- The icosahedral RNA virus as a grotto: organizing the genome into stalagmites and stalactites.Journal of biological physics · 2013Review
- Global organization of a positive-strand RNA virus genome.PLoS pathogens · 2013Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Satellite tobacco mosaic virus (STMV) is a T = 1 icosahedral virus with a single-stranded RNA genome. It is widely accepted that the RNA genome plays an important structural role during assembly of the STMV virion. While the encapsidated form of the RNA has been extensively studied, less is known about the structure of the free RNA, aside from a purported tRNA-like structure at the 3' end. Here we use selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis to examine the secondary structure of in vitro transcribed STMV RNA. The predicted secondary structure is unusual in the sense that it is highly extended, which could be significant for protecting the RNA from degradation. The SHAPE data are also consistent with the previously predicted tRNA-like fold at the 3' end of the molecule, which is also known to hinder degradation. Our data are not consistent with the secondary structure proposed for the encapsidated RNA by Schroeder et al., suggesting that, if the Schroeder structure is correct, either the RNA is packaged as it emerges from the replication complex, or the RNA undergoes extensive refolding upon encapsidation. We also consider the alternative, i.e., that the structure of the encapsidated STMV RNA might be the same as the in vitro structure presented here, and we examine how this structure might be organized in the virus. This possibility is not rigorously ruled out by the available data, so it remains open to examination by experiment.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.