ArticleQuarterly reviews of biophysics2016
Bridging the gap between in vitro and in vivo RNA folding.
Article in Quarterly reviews of biophysics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed, 142 citations in OpenAlex.
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- Alternative probe chemistries for single-molecule analysis of long noncoding RNA.The Journal of biological chemistry · 2026Article
- Systematic Evaluation of Different Ribonucleoprotein Complexes as Posttranscriptional Biosensors in Cell-Free TX-TL Systems.ACS synthetic biology · 2026Article
- Decoding the Structural Complexity of Viral RNAs with SHAPE to Guide Antiviral Therapeutics.Viruses · 2026Review
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- Mimetics of in-cell and subcellular crowding and solvation for protein folding.Biochemical Society transactions · 2026Review
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Alternative probe chemistries for single-molecule analysis of long non-coding RNA.bioRxiv : the preprint server for biology · 2026Article
- Single-molecule force measurements show that r-proteins assist 23S rRNA co-transcriptional folding.Biophysical journal · 2026Article
- Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing.bioRxiv : the preprint server for biology · 2026Article
- Prevalence of dual-donating amines in key regions of functional RNAs.RNA (New York, N.Y.) · 2025Article
- RNAtive to recognize native-like structure in a set of RNA 3D models.Bioinformatics (Oxford, England) · 2025Article
- LncRNA SChLAP1 Promotes Cancer Cell Proliferation and Invasion Via Its Distinct Structural Domains and Conserved Regions.Journal of molecular biology · 2025Article
- RNA elements and their biotechnological applications in plants.The New phytologist · 2025Review
- Transcription reshapes RNA hairpin folding pathways revealed by all-atom molecular dynamics simulations.PLoS computational biology · 2025Article
- High-throughput competitive binding assay for targeting RNA tertiary structures with small molecules: application to pseudoknots and G-quadruplexes.Nucleic acids research · 2025Article
- Structure and biochemistry-guided engineering of an all-RNA system for DNA insertion with R2 retrotransposons.Nature communications · 2025Article
- The pseudoknot structure of a viral RNA reveals a conserved mechanism for programmed exoribonuclease resistance.bioRxiv : the preprint server for biology · 2024Article
- RNA ensembles from in vitro to in vivo: Toward predictive models of RNA cellular function.Current opinion in structural biology · 2024Review
32 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Deciphering the folding pathways and predicting the structures of complex three-dimensional biomolecules is central to elucidating biological function. RNA is single-stranded, which gives it the freedom to fold into complex secondary and tertiary structures. These structures endow RNA with the ability to perform complex chemistries and functions ranging from enzymatic activity to gene regulation. Given that RNA is involved in many essential cellular processes, it is critical to understand how it folds and functions in vivo. Within the last few years, methods have been developed to probe RNA structures in vivo and genome-wide. These studies reveal that RNA often adopts very different structures in vivo and in vitro, and provide profound insights into RNA biology. Nonetheless, both in vitro and in vivo approaches have limitations: studies in the complex and uncontrolled cellular environment make it difficult to obtain insight into RNA folding pathways and thermodynamics, and studies in vitro often lack direct cellular relevance, leaving a gap in our knowledge of RNA folding in vivo. This gap is being bridged by biophysical and mechanistic studies of RNA structure and function under conditions that mimic the cellular environment. To date, most artificial cytoplasms have used various polymers as molecular crowding agents and a series of small molecules as cosolutes. Studies under such in vivo-like conditions are yielding fresh insights, such as cooperative folding of functional RNAs and increased activity of ribozymes. These observations are accounted for in part by molecular crowding effects and interactions with other molecules. In this review, we report milestones in RNA folding in vitro and in vivo and discuss ongoing experimental and computational efforts to bridge the gap between these two conditions in order to understand how RNA folds in the cell.
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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.