ArticleNucleic acids research2013
In-gel probing of individual RNA conformers within a mixed population reveals a dimerization structural switch in the HIV-1 leader.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 59 citations in OpenAlex.
- DEAD-box helicase intrinsically disordered domains and structural dynamics of HIV-1 RNA are required to reveal DDX3X catalytic efficiency.Nucleic acids research · 2025Article
- Transcription start site choice regulates HIV-1 RNA conformation and function.Current opinion in structural biology · 2024Review
- Stable structures or PABP1 loading protects cellular and viral RNAs against ISG20-mediated decay.Life science alliance · 2024Article
- Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p.RNA (New York, N.Y.) · 2023Article
- Distinct Gag interaction properties of HIV-1 RNA 5' leader conformers reveal a mechanism for dimeric genome selection.RNA (New York, N.Y.) · 2023Article
- Sequestering the 5'-cap for viral RNA packaging.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Article
- Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging.Nature structural & molecular biology · 2022Article
- A novel role for gag as a cis-acting element regulating RNA structure, dimerization and packaging in HIV-1 lentiviral vectors.Nucleic acids research · 2022Article
- Selective packaging of HIV-1 RNA genome is guided by the stability of 5' untranslated region polyA stem.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- HIV-1 Packaging Visualised by In-Gel SHAPE.Viruses · 2021Article
- Review
- The three-way junction structure of the HIV-1 PBS-segment binds host enzyme important for viral infectivity.Nucleic acids research · 2021Article
- Development of a Novel Competitive qRT-PCR Assay to Measure Relative Lentiviral Packaging Efficiency.Molecular therapy. Methods & clinical development · 2020Article
- RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures.Briefings in bioinformatics · 2020Review
- HIV-1 spliced RNAs display transcription start site bias.RNA (New York, N.Y.) · 2020Article
- Review
- Challenges and perspectives for structural biology of lncRNAs-the example of the Xist lncRNA A-repeats.Journal of molecular cell biology · 2019Article
- Intrinsic conformational dynamics of the HIV-1 genomic RNA 5'UTR.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Polymorphisms in KSHV-encoded microRNA sequences affect levels of mature viral microRNA in Kaposi Sarcoma lesions.Oncotarget · 2018Article
- An RNA-binding compound that stabilizes the HIV-1 gRNA packaging signal structure and specifically blocks HIV-1 RNA encapsidation.Retrovirology · 2018Article
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Authors and funding
4 authors at 1 institution in 1 country.
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Abstract
Definitive secondary structural mapping of RNAs in vitro can be complicated by the presence of more than one structural conformer or multimerization of some of the molecules. Until now, probing a single structure of conformationally flexible RNA molecules has typically relied on introducing stabilizing mutations or adjusting buffer conditions or RNA concentration. Here, we present an in-gel SHAPE (selective 2'OH acylation analysed by primer extension) approach, where a mixed structural population of RNA molecules is separated by non-denaturing gel electrophoresis and the conformers are individually probed within the gel matrix. Validation of the technique using a well-characterized RNA stem-loop structure, the HIV-1 trans-activation response element, showed that authentic structure was maintained and that the method was accurate and highly reproducible. To further demonstrate the utility of in-gel SHAPE, we separated and examined monomeric and dimeric species of the HIV-1 packaging signal RNA. Extensive differences in acylation sensitivity were seen between monomer and dimer. The results support a recently proposed structural switch model of RNA genomic dimerization and packaging, and demonstrate the discriminatory power of in-gel SHAPE.
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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.