ArticlePloS one2014
Viral RNAs are unusually compact.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- Periodic genome sequences facilitate packaging in a single-stranded DNA virus.Journal of virology · 2026Article
- Structural organization of HBV pgRNA genome driven by phase separation in capsid confinement.Nature communications · 2026Article
- A naturally occurring NS1 variant with effector domain deletion gains growth advantages in influenza virus infection.Emerging microbes & infections · 2025Article
- New rhinovirus uncoating intermediate reveals how sodium versus potassium ions influence RNA release.Scientific reports · 2025Article
- Measuring the selective packaging of RNA molecules by viral coat proteins in cells.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- Molecular Dynamics Characterization of the Free and Encapsidated RNA2 of CCMV with the oxRNA Model.Macromolecular rapid communications · 2024Article
- Disenfranchised DNA: biochemical analysis of mutant øX174 DNA-binding proteins may further elucidate the evolutionary significance of the unessential packaging protein A.Journal of virology · 2024Article
- Long ssRNA undergoes continuous compaction in the presence of polyvalent cations.Biophysical journal · 2023Article
- Directed Evolution of Seneca Valley Virus in Tumorsphere and Monolayer Cell Cultures of a Small-Cell Lung Cancer Model.Cancers · 2023Article
- Conformational dynamics and energetics of viral RNA recognition by lab-evolved proteins.Physical chemistry chemical physics : PCCP · 2021Article
- Theoretical basis for stabilizing messenger RNA through secondary structure design.Nucleic acids research · 2021Article
- Relationships between RNA topology and nucleocapsid structure in a model icosahedral virus.Biophysical journal · 2021Article
- Review
- The Effects of Packaged, but Misguided, Single-Stranded DNA Genomes Are Transmitted to the Outer Surface of the ϕX174 Capsid.Journal of virology · 2021Article
- Virus Mechanics under Molecular Crowding.The journal of physical chemistry. B · 2021Article
- Theoretical basis for stabilizing messenger RNA through secondary structure design.bioRxiv : the preprint server for biology · 2021Article
- Physics of viral dynamics.Nature reviews. Physics · 2021Review
- Visualizing a viral genome with contrast variation small angle X-ray scattering.The Journal of biological chemistry · 2020Article
- Finally, a Role Befitting AJournal of virology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A majority of viruses are composed of long single-stranded genomic RNA molecules encapsulated by protein shells with diameters of just a few tens of nanometers. We examine the extent to which these viral RNAs have evolved to be physically compact molecules to facilitate encapsulation. Measurements of equal-length viral, non-viral, coding and non-coding RNAs show viral RNAs to have among the smallest sizes in solution, i.e., the highest gel-electrophoretic mobilities and the smallest hydrodynamic radii. Using graph-theoretical analyses we demonstrate that their sizes correlate with the compactness of branching patterns in predicted secondary structure ensembles. The density of branching is determined by the number and relative positions of 3-helix junctions, and is highly sensitive to the presence of rare higher-order junctions with 4 or more helices. Compact branching arises from a preponderance of base pairing between nucleotides close to each other in the primary sequence. The density of branching represents a degree of freedom optimized by viral RNA genomes in response to the evolutionary pressure to be packaged reliably. Several families of viruses are analyzed to delineate the effects of capsid geometry, size and charge stabilization on the selective pressure for RNA compactness. Compact branching has important implications for RNA folding and viral assembly.
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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.