ArticleNucleic acids research2007
Encoding folding paths of RNA switches.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 52 citations in OpenAlex.
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Design and discovery of 'tug-of-war' riboswitches.bioRxiv : the preprint server for biology · 2026Article
- StraD: a coarse-grained simulation of co-transcriptional RNA folding.NAR genomics and bioinformatics · 2025Article
- Tissue-specific modulation of CRISPR activity by miRNA-sensing guide RNAs.Nucleic acids research · 2025Article
- DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model.Bioinformatics (Oxford, England) · 2023Article
- The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements.Nucleic acids research · 2021Article
- Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis.Biophysical journal · 2019Article
- Self-powered RNA nanomachine driven by metastable structure.Nucleic acids research · 2019Article
- Viroid research and its significance for RNA technology and basic biochemistry.Nucleic acids research · 2018Review
- Predicting Cotranscriptional Folding Kinetics For Riboswitch.The journal of physical chemistry. B · 2018Article
- Design of Artificial Riboswitches as Biosensors.Sensors (Basel, Switzerland) · 2017Review
- Efficient approximations of RNA kinetics landscape using non-redundant sampling.Bioinformatics (Oxford, England) · 2017Article
- Pseudoknots in RNA folding landscapes.Bioinformatics (Oxford, England) · 2016Article
- Creating small transcription activating RNAs.Nature chemical biology · 2015Article
- The purine riboswitch as a model system for exploring RNA biology and chemistry.Biochimica et biophysica acta · 2014Review
- Single-molecule studies of riboswitch folding.Biochimica et biophysica acta · 2014Review
- Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.Bioinformatics (Oxford, England) · 2014Article
- Advances in methods for native expression and purification of RNA for structural studies.Current opinion in structural biology · 2014Review
- Engineering modular 'ON' RNA switches using biological components.Nucleic acids research · 2013Article
- The centrality of RNA for engineering gene expression.Biotechnology journal · 2013Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions (UTRs). Yet, the underlying mechanisms and coding requirements for efficient co-transcriptional folding remain unclear. Traditional approaches have intrinsic limitations to dissect RNA folding paths, as they rely on sequence mutations or circular permutations that typically perturb both RNA folding paths and equilibrium structures. Here, we show that exploiting sequence symmetries instead of mutations can circumvent this problem by essentially decoupling folding paths from equilibrium structures of designed RNA sequences. Using bistable RNA switches with symmetrical helices conserved under sequence reversal, we demonstrate experimentally that native and transiently formed helices can guide efficient co-transcriptional folding into either long-lived structure of these RNA switches. Their folding path is controlled by the order of helix nucleations and subsequent exchanges during transcription, and may also be redirected by transient antisense interactions. Hence, transient intra- and inter-molecular base pair interactions can effectively regulate the folding of nascent RNA molecules into different native structures, provided limited coding requirements, as discussed from an information theory perspective. This constitutive coupling between RNA synthesis and RNA folding regulation may have enabled the early emergence of autonomous RNA-based regulation networks.
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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.