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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
doaj   +2 more sources

Computational modeling of cotranscriptional RNA folding [PDF]

Computational and Structural Biotechnology Journal
An 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
doaj   +2 more sources

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
doaj   +2 more sources

Ab initio RNA folding [PDF]

Journal of Physics: Condensed Matter, 2014
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray crystallography and
Cragnolini, Tristan, Derreumaux, Philippe, Pasquali, Samuela   +2 more
core   +5 more sources

Statistical Physics of RNA-folding [PDF]

Physical Review E, 2002
We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops.
Mueller, M.
core   +5 more sources

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
doaj   +2 more sources

Sequential structure probing of cotranscriptional RNA folding intermediates [PDF]

Nature Communications
Cotranscriptional 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, Skyler L. Kelly, Eric J. Strobel   +2 more
doaj   +2 more sources

Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect

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, Yao Liu, Zizhang Li, Shuyun Deng, Zhuoxing Wu, Xiaoyu Zhang, Wenbo Chen, Junnan Yang, Xiaoshu Chen, Jian-Rong Yang   +9 more
doaj   +2 more sources

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, Christopher M MacDermaid, Andrea M A Schreij, Magdalena Zwierzyna, Ross C Walker   +4 more
doaj   +2 more sources

Inverse folding of RNA pseudoknot structures [PDF]

Algorithms for Molecular Biology, 2010
Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure) and additional cross-serial base pairs.
Li Linda YM, Gao James ZM, Reidys Christian M   +2 more
doaj   +2 more sources