ArticleRNA (New York, N.Y.)2013
QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis.
Article in RNA (New York, N.Y.), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers.
What it found
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Who cites it
146 citing papers in PubMed.
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- The SL-I structural element of the 3' UTR region of West Nile virus participates in the regulation of viral translation.The Journal of general virology · 2026Article
- Nucleotide-Resolution Mapping Reveals Specific MLE Binding Site on roX2 lncRNA.Journal of molecular biology · 2026Article
- Evolutionary refinement of the ZIKV 5' UTR dictates a trade-off between RNA stability and promoter accessibility.NAR molecular medicine · 2026Article
- Cleavage region organizes the structural architecture of the SINE-derived B2 repressive ribozyme.Communications biology · 2026Article
- Identification and comparison of RNA structures in 5'- and 3'-terminal genomic regions across four coronavirus genera by SHAPE analysis.Virology journal · 2026Article
- Mapping the RNA Chaperone Activity of the Trypanosoma brucei Editosome Using SHAPE-Chemical Probing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Structural and functional characterization of the SLA' structure at the 3' terminus of the Zika virus negative-strand intermediate.RNA (New York, N.Y.) · 2025Article
- A cohort of mRNAs undergo high-stoichiometry NSUN6-mediated site-specific mNature communications · 2025Article
- A structural element within the 5'UTR of β-catenin mRNA modulates its translation under hypoxia.Nucleic acids research · 2025Article
- IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.NAR genomics and bioinformatics · 2025Article
- Non-AUG HIV-1 uORF translation elicits specific T cell immune response and regulates viral transcript expression.Nature communications · 2025Article
- Zika viruses encode 5' upstream open reading frames affecting infection of human brain cells.Nature communications · 2024Article
- A specific domain within the 3' untranslated region of Usutu virus confers resistance to the exonuclease ISG20.Nature communications · 2024Article
- MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals.PLoS biology · 2024Article
- Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes.Nucleic acids research · 2024Article
- Structural Impact of the Interaction of the Influenza A Virus Nucleoprotein with Genomic RNA Segments.Viruses · 2024Article
- A compact regulatory RNA element in mouse Hsp70 mRNA.NAR molecular medicine · 2024Article
- RNA Secondary Structure Modeling Following the IPANEMAP Workflow.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging.RNA (New York, N.Y.) · 2023Article
86 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Chemical probing of RNA and DNA structure is a widely used and highly informative approach for examining nucleic acid structure and for evaluating interactions with protein and small-molecule ligands. Use of capillary electrophoresis to analyze chemical probing experiments yields hundreds of nucleotides of information per experiment and can be performed on automated instruments. Extraction of the information from capillary electrophoresis electropherograms is a computationally intensive multistep analytical process, and no current software provides rapid, automated, and accurate data analysis. To overcome this bottleneck, we developed a platform-independent, user-friendly software package, QuShape, that yields quantitatively accurate nucleotide reactivity information with minimal user supervision. QuShape incorporates newly developed algorithms for signal decay correction, alignment of time-varying signals within and across capillaries and relative to the RNA nucleotide sequence, and signal scaling across channels or experiments. An analysis-by-reference option enables multiple, related experiments to be fully analyzed in minutes. We illustrate the usefulness and robustness of QuShape by analysis of RNA SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experiments.
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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.