ArticleBiochemistry2015
Challenge of mimicking the influences of the cellular environment on RNA structure by PEG-induced macromolecular crowding.
Article in Biochemistry, 2015. 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, 73 citations in OpenAlex.
- Nearest Neighbor Parameters for Estimating RNA Folding Stability withbioRxiv : the preprint server for biology · 2026Article
- Protein crowders remodel RNA electrostatics, hydration, and dynamics: a challenge to steric crowding models.Nucleic acids research · 2026Article
- Article
- RNA circularization preserves dynamics and enables in-cell relaxation NMR.Nucleic acids research · 2026Article
- Residue-level mapping of crowding effects on protein phase separation.Protein science : a publication of the Protein Society · 2026Article
- Cell flocculation and phase-separation support macro-scale tissue slab construction in a scaffold-free manner.Materials today. Bio · 2026Article
- Catalyst-Free Collagen Filament Crosslinking for Engineering Anisotropic and Mechanically Robust Tissue Scaffolds.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Article
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- Protocell Effects on RNA Folding, Function, and Evolution.Accounts of chemical research · 2024Article
- Constrained dynamics of DNA oligonucleotides in phase-separated droplets.Biophysical journal · 2024Article
- Technologies for studying phase-separated biomolecular condensates.Advanced biotechnology · 2024Review
- In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells.Nucleic acids research · 2023Article
- Macromolecular Crowding Is Surprisingly Unable to Deform the Structure of a Model Biomolecular Condensate.Biology · 2023Article
- The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability.Biochemistry · 2022Article
- Zeptoliter DNA Origami Reactor to Reveal Cosolute Effects on Nanoconfined G-Quadruplexes.The journal of physical chemistry letters · 2022Article
- Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence.Molecules (Basel, Switzerland) · 2022Article
- Stability and Activity of the 10-23 DNAzyme Under Molecular Crowding Conditions.Methods in molecular biology (Clifton, N.J.) · 2022Article
- RNA sequence and structure control assembly and function of RNA condensates.RNA (New York, N.Y.) · 2021Article
- A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
There are large differences between the cellular environment and the conditions widely used to study RNA in vitro. SHAPE RNA structure probing in Escherichia coli cells has shown that the cellular environment stabilizes both long-range and local tertiary interactions in the adenine riboswitch aptamer domain. Synthetic crowding agents are widely used to understand the forces that stabilize RNA structure and in efforts to recapitulate the cellular environment under simplified experimental conditions. Here, we studied the structure and ligand binding ability of the adenine riboswitch in the presence of the macromolecular crowding agent, polyethylene glycol (PEG). Ethylene glycol and low-molecular mass PEGs destabilized RNA structure and caused the riboswitch to sample secondary structures different from those observed in simple buffered solutions or in cells. In the presence of larger PEGs, longer-range loop-loop interactions were more similar to those in cells than in buffer alone, consistent with prior work showing that larger PEGs stabilize compact RNA states. Ligand affinity was weakened by low-molecular mass PEGs but increased with high-molecular mass PEGs, indicating that PEG cosolvents exert complex chemical and steric effects on RNA structure. Regardless of polymer size, however, nucleotide-resolution structural characteristics observed in cells were not recapitulated in PEG solutions. Our results reveal that the cellular environment is difficult to recapitulate in vitro; mimicking the cellular state will likely require a combination of crowding agents and other chemical species.
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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.