ArticleMethods (San Diego, Calif.)2016
Probing the structure of ribosome assembly intermediates in vivo using DMS and hydroxyl radical footprinting.
Article in Methods (San Diego, Calif.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Anti-sense oligonucleotide probing as a structural platform for studying ribonucleoprotein complex assembly.Nature communications · 2025Article
- Domain consolidation in Bacterial 50S assembly revealed by Anti-Sense Oligonucleotide Probing.bioRxiv : the preprint server for biology · 2024Article
- Late consolidation of rRNA structure during co-transcriptional assembly inbioRxiv : the preprint server for biology · 2024Article
- Photochemical and Single Electron Transfer Generation of 2'-Deoxycytidin-The Journal of organic chemistry · 2023Article
- Emerging Quantitative Biochemical, Structural, and Biophysical Methods for Studying Ribosome and Protein-RNA Complex Assembly.Biomolecules · 2023Review
- Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Hydroxyl radical mediated damage of proteins in low oxygen solution investigated using X-ray footprinting mass spectrometry.Journal of synchrotron radiation · 2021Article
- Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications.Chemical reviews · 2020Review
- The chemistry and applications of RNA 2'-OH acylation.Nature reviews. Chemistry · 2020Article
- Coordinated Control of rRNA Processing by RNA Polymerase I.Trends in genetics : TIG · 2019Review
- The XFP (17-BM) beamline for X-ray footprinting at NSLS-II.Journal of synchrotron radiation · 2019Article
- Assaying RNA structure with LASER-Seq.Nucleic acids research · 2019Article
- Recent Advances in X-Ray Hydroxyl Radical Footprinting at the Advanced Light Source Synchrotron.Protein and peptide letters · 2019Article
- Time-Resolved Hydroxyl Radical Footprinting of RNA with X-Rays.Current protocols in nucleic acid chemistry · 2018Article
- Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment.Molecular & cellular proteomics : MCP · 2017Review
- Toward Time-Resolved Analysis of RNA Metabolism in Archaea Using 4-Thiouracil.Frontiers in microbiology · 2017Article
- Advances in RNA structure determination.Methods (San Diego, Calif.) · 2016Article
Corrections and comments
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
The assembly of the Escherichia coli ribosome has been widely studied and characterized in vitro. Despite this, ribosome biogenesis in living cells is only partly understood because assembly is coupled with transcription, modification and processing of the pre-ribosomal RNA. We present a method for footprinting and isolating pre-rRNA as it is synthesized in E. coli cells. Pre-rRNA synthesis is synchronized by starvation, followed by nutrient upshift. RNA synthesized during outgrowth is metabolically labeled to facilitate isolation of recent transcripts. Combining this technique with two in vivo RNA probing methods, hydroxyl radical and DMS footprinting, allows the structure of nascent RNA to be probed over time. Together, these can be used to determine changes in the structures of ribosome assembly intermediates as they fold in vivo.
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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.