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Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing [PDF]
Nature Communications, 2023 RNA begins to fold as it is transcribed by an RNA polymerase. Consequently, RNA folding is constrained by the direction and rate of transcription.
Courtney E. Szyjka, Eric J. Strobel
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Computational modeling of cotranscriptional RNA folding [PDF]
Computational and Structural Biotechnology JournalAn RNA folds as it is transcribed. RNA folding during transcription differs fundamentally from thermodynamic folding. While thermodynamic folding reaches an equilibrium ensemble of structures, cotranscriptional folding is a kinetic process where the RNA ...
Lei Jin, Shi-Jie Chen
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Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search [PDF]
Molecules, 2021 RNA molecules participate in many important biological processes, and they need to fold into well-defined secondary and tertiary structures to realize their functions. Like the well-known protein folding problem, there is also an RNA folding problem. The
Kangkun Mao, Yi Xiao
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Nature Communications, 2023 The transcriptional intermediates of RNAs fold into secondary structures with multiple regulatory roles, yet the details of such cotranscriptional RNA folding are largely unresolved in eukaryotes.
Gongwang Yu +9 more
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Sequential structure probing of cotranscriptional RNA folding intermediates [PDF]
Nature CommunicationsCotranscriptional RNA folding pathways typically involve the sequential formation of folding intermediates. Existing methods for cotranscriptional RNA structure probing map the structure of nascent RNA in the context of a terminally arrested ...
Courtney E. Szyjka +2 more
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RNA folding and functions of RNA helicases in ribosome biogenesis [PDF]
RNA Biology, 2022 Eukaryotic ribosome biogenesis involves the synthesis of ribosomal RNA (rRNA) and its stepwise folding into the unique structure present in mature ribosomes.
Valentin Mitterer, Brigitte Pertschy
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RNA folding using quantum computers. [PDF]
PLoS Computational Biology, 2022 The 3-dimensional fold of an RNA molecule is largely determined by patterns of intramolecular hydrogen bonds between bases. Predicting the base pairing network from the sequence, also referred to as RNA secondary structure prediction or RNA folding, is a
Dillion M Fox +4 more
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RNA folding kinetics control riboswitch sensitivity in vivo [PDF]
Nature CommunicationsRiboswitches are ligand-responsive gene-regulatory RNA elements that perform key roles in maintaining cellular homeostasis. Understanding how riboswitch sensitivity to ligand (EC50) is controlled is critical to explain how highly conserved aptamer ...
David Z. Bushhouse +2 more
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Hidden Structural Modules in a Cooperative RNA Folding Transition
Cell Reports, 2018 Summary: Large-scale, cooperative rearrangements underlie the functions of RNA in RNA-protein machines and gene regulation. To understand how such rearrangements are orchestrated, we used high-throughput chemical footprinting to dissect a seemingly ...
Brant Gracia +5 more
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RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform. [PDF]
PLoS Computational Biology, 2022 We propose a novel heuristic to predict RNA secondary structure formation pathways that has two components: (i) a folding algorithm and (ii) a kinetic ansatz.
Vaitea Opuu +3 more
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