ArticleBiophysical journal2011
Ensemble of secondary structures for encapsidated satellite tobacco mosaic virus RNA consistent with chemical probing and crystallography constraints.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 42 citations in OpenAlex.
- Periodic genome sequences facilitate packaging in a single-stranded DNA virus.Journal of virology · 2026Article
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- Universal and strain specific structure features of segment 8 genomic RNA of influenza A virus-application of 4-thiouridine photocrosslinking.The Journal of biological chemistry · 2021Article
- Review
- Challenges and approaches to predicting RNA with multiple functional structures.RNA (New York, N.Y.) · 2018Review
- Swellix: a computational tool to explore RNA conformational space.BMC bioinformatics · 2017Article
- Influenza virus segment 5 (+)RNA - secondary structure and new targets for antiviral strategies.Scientific reports · 2017Article
- Packaged and Free Satellite Tobacco Mosaic Virus (STMV) RNA Genomes Adopt Distinct Conformational States.Biochemistry · 2017Article
- Article
- Biologically-supported structural model for a viral satellite RNA.Nucleic acids research · 2015Article
- Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix.The journal of physical chemistry. B · 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
- Asymmetric genome organization in an RNA virus revealed via graph-theoretical analysis of tomographic data.PLoS computational biology · 2015Article
- Article
- Microarrays for identifying binding sites and probing structure of RNAs.Nucleic acids research · 2015Review
- Long-range architecture in a viral RNA genome.Biochemistry · 2013Article
- To build a virus on a nucleic acid substrate.Biophysical journal · 2013Article
- Visualizing RNA base-pairing probabilities with RNAbow diagrams.RNA (New York, N.Y.) · 2013Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viral genomic RNA adopts many conformations during its life cycle as the genome is replicated, translated, and encapsidated. The high-resolution crystallographic structure of the satellite tobacco mosaic virus (STMV) particle reveals 30 helices of well-ordered RNA. The crystallographic data provide global constraints on the possible secondary structures for the encapsidated RNA. Traditional free energy minimization methods of RNA secondary structure prediction do not generate structures consistent with the crystallographic data, and to date no complete STMV RNA basepaired secondary structure has been generated. RNA-protein interactions and tertiary interactions may contribute a significant degree of stability, and the kinetics of viral assembly may dominate the folding process. The computational tools, Helix Find & Combine, Crumple, and Sliding Windows and Assembly, evaluate and explore the possible secondary structures for encapsidated STMV RNA. All possible hairpins consistent with the experimental data and a cotranscriptional folding and assembly hypothesis were generated, and the combination of hairpins that was most consistent with experimental data is presented as the best representative structure of the ensemble. Multiple solutions to the genome packaging problem could be an evolutionary advantage for viruses. In such cases, an ensemble of structures that share favorable global features best represents the RNA fold.
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Registered trials
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.