Cotranscriptional Kinetic Folding of RNA Secondary Structures Including Pseudoknots

Thanh, Vo Hong; Korpela, Dani; Orponen, Pekka

doi:10.1089/cmb.2020.0606

Cited by 3 publications

(2 citation statements)

References 42 publications

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“…The software discussed here is only a part of generally available cotranscriptional folding software. Among other cotranscriptional folding simulators are Kinefold [38], RNAkinetics [39], Kinwalker [40], BarMap [41], and CoStochFold [42]. The drconverters repository provides a script to convert results from Kinefold to the .drf file format.…”

Section: Discussionmentioning

confidence: 99%

A guide to computational cotranscriptional folding featuring the SRP RNA

Badelt

Lorenz

2023

Preprint

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Although RNA molecules are synthesized via transcription, little is known about the general impact of cotranscriptional folding in vivo. We present different computational approaches for the simulation of changing structure ensembles during transcription, including interpretations with respect to experimental data from literature. Specifically, we analyze different mutations of the E.coli SRP RNA, which has been studied comparatively well in previous literature, yet the details of which specific metastable structures form, as well as when they form are still under debate. Here, we combine thermodynamic and kinetic, deterministic and stochastic models with automated and visual inspection of those systems to derive the most likely scenario of which substructures form at which point during transcription. The simulations do not only provide explanations for present experimental observations, but also suggest previously unnoticed conformations that may be verified through future experimental studies.

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Section: Discussionmentioning

confidence: 99%

A guide to computational cotranscriptional folding featuring the SRP RNA

Badelt

Lorenz

2023

Preprint

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“…Even if only two structures dominate the ensemble in terms of occupancy, many more intermediate structures may have to be included in a model to estimate the dynamics between these two structures. Among existing algorithms are stochastic simulations ( ( Flamm et al , 2000 ), ( Xayaphoummine et al , 2005 ), ( Danilova et al , 2006 ), ( Thanh et al , 2021 )], master equation methods [ ( Hofacker et al , 2010 ), theoretical work from Zhao et al (2011) ], the deterministic prediction of a single folding trajectory [ ( Geis et al , 2008 )], as well as a recent model to interpret experimental data ( Yu et al , 2021 ) and theoretical work on combining stochastic modeling with deterministic helix kinetics ( Xu et al , 2022 ).…”

Section: Introductionmentioning

confidence: 99%

`DrTransformer`: heuristic cotranscriptional RNA folding using the nearest neighbor energy model

2023

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Background Folding during transcription can have an important influence on the structure and function of RNA molecules, as regions closer to the 5’ end can fold into metastable structures before potentially stronger interactions with the 3’ end become available. Thermodynamic RNA folding models are not suitable to predict structures that result from cotranscriptional folding, as they can only calculate properties of the equilibrium distribution. Other software packages that simulate the kinetic process of RNA folding during transcription exist, but they are mostly applicable for short sequences. Results We present a new algorithm that tracks changes to the RNA secondary structure ensemble during transcription. At every transcription step, new representative local minima are identified, a neighborhood relation is defined and transition rates are estimated for kinetic simulations. After every simulation, a part of the ensemble is removed and the remainder is used to search for new representative structures. The presented algorithm is deterministic (up to numeric instabilities of simulations), fast (in comparison with existing methods), and it is capable of folding RNAs much longer than 200 nucleotides. Availability This software is open-source and available at https://github.com/ViennaRNA/drtransformer. Supplementary information Supplementary data are available at Bioinformatics online.

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A Guide to Computational Cotranscriptional Folding Featuring the SRP RNA

Badelt,

Lorenz

2012

Methods in Molecular Biology

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Cotranscriptional Kinetic Folding of RNA Secondary Structures Including Pseudoknots

Cited by 3 publications

References 42 publications

A guide to computational cotranscriptional folding featuring the SRP RNA

A guide to computational cotranscriptional folding featuring the SRP RNA

`DrTransformer`: heuristic cotranscriptional RNA folding using the nearest neighbor energy model

A Guide to Computational Cotranscriptional Folding Featuring the SRP RNA

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Cotranscriptional Kinetic Folding of RNA Secondary Structures Including Pseudoknots

Cited by 3 publications

References 42 publications

A guide to computational cotranscriptional folding featuring the SRP RNA

A guide to computational cotranscriptional folding featuring the SRP RNA

DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model

A Guide to Computational Cotranscriptional Folding Featuring the SRP RNA

Contact Info

Product

Resources

About

`DrTransformer`: heuristic cotranscriptional RNA folding using the nearest neighbor energy model