ArticleBiochemistry2013
The cellular environment stabilizes adenine riboswitch RNA structure.
Article in Biochemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
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Who cites it
83 citing papers in PubMed.
- Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models.Nucleic acids research · 2026Article
- RNA circularization preserves dynamics and enables in-cell relaxation NMR.Nucleic acids research · 2026Article
- Beyond the niche - unlocking the full potential of synthetic riboswitches.Nature communications · 2025Review
- Rapid CRISPR-Cas9 target-strand nicking can provide phage resistance by reducing DNA abundance.Nucleic acids research · 2025Article
- Modeling riboswitches: The impact of concentration of MgBiophysical journal · 2025Article
- Review
- Reentrant DNA shells tune polyphosphate condensate size.Nature communications · 2024Article
- CRISPR-Cas12a exhibits metal-dependent specificity switching.Nucleic acids research · 2024Article
- The application of single-molecule optical tweezers to study disease-related structural dynamics in RNA.Biochemical Society transactions · 2024Review
- 2'-OH as a universal handle for studying intracellular RNAs.Cell chemical biology · 2024Review
- CRISPR-Cas12a exhibits metal-dependent specificity switching.bioRxiv : the preprint server for biology · 2024Article
- Direct observation of tRNA-chaperoned folding of a dynamic mRNA ensemble.Nature communications · 2023Article
- Disentangling contact and ensemble epistasis in a riboswitch.Biophysical journal · 2023Article
- Magnesium Modulates Bacillus subtilis Cell Division Frequency.Journal of bacteriology · 2023Article
- Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors.Marine life science & technology · 2022Review
- Repurposing an adenine riboswitch into a fluorogenic imaging and sensing tag.Nature chemical biology · 2022Article
- Combining Coarse-Grained Simulations and Single Molecule Analysis Reveals a Three-State Folding Model of the Guanidine-II Riboswitch.Frontiers in molecular biosciences · 2022Article
- Multiplexed assessment of engineered bacterial constructs for intracellular β-galactosidase expression by redox amplification on catechol-chitosan modified nanoporous gold.Mikrochimica acta · 2021Article
- An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel.Communications biology · 2021Article
- Review
23 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
There are large differences between the intracellular environment and the conditions widely used to study RNA structure and function in vitro. To assess the effects of the crowded cellular environment on RNA, we examined the structure and ligand binding function of the adenine riboswitch aptamer domain in healthy, growing Escherichia coli cells at single-nucleotide resolution on the minute time scale using SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension). The ligand-bound aptamer structure is essentially the same in cells and in buffer at 1 mM Mg(2+), the approximate Mg(2+) concentration we measured in cells. In contrast, the in-cell conformation of the ligand-free aptamer is much more similar to the fully folded ligand-bound state. Even adding high Mg(2+) concentrations to the buffer used for in vitro analyses did not yield the conformation observed for the free aptamer in cells. The cellular environment thus stabilizes the aptamer significantly more than does Mg(2+) alone. Our results show that the intracellular environment has a large effect on RNA structure that ultimately favors highly organized conformations.
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