ArticleNucleic acids research2008
High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 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.
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Who cites it
64 citing papers in PubMed.
- IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.NAR genomics and bioinformatics · 2025Article
- Modeling the structure and DAP5-binding site of the FGF-9 5'-UTR RNA utilized in cap-independent translation.RNA (New York, N.Y.) · 2024Article
- RNA Secondary Structure Modeling Following the IPANEMAP Workflow.Methods in molecular biology (Clifton, N.J.) · 2024Article
- RNA Chemical Labeling with Site-Specific, Relative Quantification by Mass Spectrometry for the Structural Study of a Neomycin-Sensing Riboswitch Aptamer Domain.ChemPlusChem · 2022Article
- Eukaryotic initiation factor 4F promotes a reorientation of eukaryotic initiation factor 3 binding on the 5' and the 3' UTRs of barley yellow dwarf virus mRNA.Nucleic acids research · 2022Article
- Review
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Classification of RNA structure change by 'gazing' at experimental data.Bioinformatics (Oxford, England) · 2017Article
- Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions.Nucleic acids research · 2017Article
- RiboCAT: a new capillary electrophoresis data analysis tool for nucleic acid probing.RNA (New York, N.Y.) · 2017Article
- Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA.Journal of medicinal chemistry · 2016Article
- A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8.Nucleic acids research · 2016Article
- Expression of Alternatively Spliced Human T-Cell Leukemia Virus Type 1 mRNAs Is Influenced by Mitosis and by a Novel cis-Acting Regulatory Sequence.Journal of virology · 2016Article
- Novel Biochemical Tools for Probing HIV RNA Structure.Methods in molecular biology (Clifton, N.J.) · 2016Article
- Probing Xist RNA Structure in Cells Using Targeted Structure-Seq.PLoS genetics · 2015Article
- Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles.Bioinformatics (Oxford, England) · 2015Article
- Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR.RNA (New York, N.Y.) · 2015Article
- Consistent global structures of complex RNA states through multidimensional chemical mapping.eLife · 2015Article
- Computational analysis of RNA structures with chemical probing data.Methods (San Diego, Calif.) · 2015Review
- Heterogeneous dynamics in DNA site discrimination by the structurally homologous DNA-binding domains of ETS-family transcription factors.Nucleic acids research · 2015Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
The use of capillary electrophoresis with fluorescently labeled nucleic acids revolutionized DNA sequencing, effectively fueling the genomic revolution. We present an application of this technology for the high-throughput structural analysis of nucleic acids by chemical and enzymatic mapping ('footprinting'). We achieve the throughput and data quality necessary for genomic-scale structural analysis by combining fluorophore labeling of nucleic acids with novel quantitation algorithms. We implemented these algorithms in the CAFA (capillary automated footprinting analysis) open-source software that is downloadable gratis from https://simtk.org/home/cafa. The accuracy, throughput and reproducibility of CAFA analysis are demonstrated using hydroxyl radical footprinting of RNA. The versatility of CAFA is illustrated by dimethyl sulfate mapping of RNA secondary structure and DNase I mapping of a protein binding to a specific sequence of DNA. Our experimental and computational approach facilitates the acquisition of high-throughput chemical probing data for solution structural analysis of nucleic acids.
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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.