ArticleThe Journal of chemical physics2011
Cotranscriptional folding kinetics of ribonucleic acid secondary structures.
Article in The Journal of chemical physics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- Computational modeling of cotranscriptional RNA folding.Computational and structural biotechnology journal · 2025Review
- Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing.Nature communications · 2023Article
- cRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities.International journal of molecular sciences · 2023Article
- DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model.Bioinformatics (Oxford, England) · 2023Article
- Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.Journal of chemical theory and computation · 2022Article
- Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions.Computational and structural biotechnology journal · 2022Review
- Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.Chemical reviews · 2021Review
- RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds.Nature chemistry · 2021Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability.Biophysical journal · 2020Article
- Effects of flanking regions on HDV cotranscriptional folding kinetics.RNA (New York, N.Y.) · 2018Article
- Predicting Cotranscriptional Folding Kinetics For Riboswitch.The journal of physical chemistry. B · 2018Article
- Computational Methods for Modeling Aptamers and Designing Riboswitches.International journal of molecular sciences · 2017Review
- Design of Artificial Riboswitches as Biosensors.Sensors (Basel, Switzerland) · 2017Review
- Integration of mRNP formation and export.Cellular and molecular life sciences : CMLS · 2017Review
- Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches.Molecules (Basel, Switzerland) · 2017Review
- Fast, approximate kinetics of RNA folding.Journal of computational biology : a journal of computational molecular cell biology · 2015Article
- Coupling mRNA processing with transcription in time and space.Nature reviews. Genetics · 2014Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We develop a systematic helix-based computational method to predict RNA folding kinetics during transcription. In our method, the transcription is modeled as stepwise process, where each step is the transcription of a nucleotide. For each step, the kinetics algorithm predicts the population kinetics, transition pathways, folding intermediates, and the transcriptional folding products. The folding pathways, rate constants, and the conformational populations for cotranscription folding show contrastingly different features than the refolding kinetics for a fully transcribed chain. The competition between the transcription speed and rate constants for the transitions between the different nascent structures determines the RNA folding pathway and the end product of folding. For example, fast transcription favors the formation of branch-like structures than rod-like structures and chain elongation in the folding process may reduce the probability of the formation of misfolded structures. Furthermore, good theory-experiment agreements suggest that our method may provide a reliable tool for quantitative prediction for cotranscriptional RNA folding, including the kinetics for the population distribution for the whole conformational ensemble.
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Registered trials
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