ArticleJournal of virology2014
Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.
Article in Journal of virology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
20 citing papers in PubMed, 38 citations in OpenAlex.
- Modulating G-quadruplexes for therapeutic intervention: Structural diversity, stability, and emerging nucleic-acid-based strategies.Molecular therapy. Nucleic acids · 2026Review
- Structural Modeling of Protein-DNA Interactions Underlying Genome Copy Number Variation in Nanoviruses.Computational and structural biotechnology journal · 2026Article
- Developing and Applying RNA Empirical Models With Secondary Structure Insights for Orthoptera Phylogenetics.Ecology and evolution · 2025Article
- The Role of a C-Terminal Seven-Amino Acid Motif in TbCSV C3 Protein and Its Interaction With NbPOLA2 in Enhancing Viral Replication.Molecular plant pathology · 2025Article
- Article
- An extended APOBEC3A mutation signature in cancer.Nature communications · 2021Article
- Evolutionary Analyses of Base-Pairing Interactions in DNA and RNA Secondary Structures.Molecular biology and evolution · 2020Article
- Argonaute bypasses cellular obstacles without hindrance during target search.Nature communications · 2019Article
- Redondoviridae, a Family of Small, Circular DNA Viruses of the Human Oro-Respiratory Tract Associated with Periodontitis and Critical Illness.Cell host & microbe · 2019Article
- Pervasive Chimerism in the Replication-Associated Proteins of Uncultured Single-Stranded DNA Viruses.Viruses · 2018Article
- Article
- The blood DNA virome in 8,000 humans.PLoS pathogens · 2017Article
- DNA secondary structure formation by DNA shuffling of the conserved domains of the Cry protein ofBMC biophysics · 2017Article
- The Strange Lifestyle of Multipartite Viruses.PLoS pathogens · 2016Review
- Impact of the MRN Complex on Adeno-Associated Virus Integration and Replication during Coinfection with Herpes Simplex Virus 1.Journal of virology · 2015Article
- Functionally conserved architecture of hepatitis C virus RNA genomes.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates.Virology journal · 2014Article
- Evolution of eukaryotic single-stranded DNA viruses of the Bidnaviridae family from genes of four other groups of widely different viruses.Scientific reports · 2014Article
- SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.PloS one · 2014Article
- Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context.PloS one · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors at 7 institutions in 6 countries.
Funding
Abstract
Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.
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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.