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Salt corrections for RNA secondary structures in the ViennaRNA package

View ORCID ProfileHua-Ting Yao, View ORCID ProfileRonny Lorenz, View ORCID ProfileIvo L. Hofacker, View ORCID ProfilePeter F. Stadler
doi: https://doi.org/10.1101/2023.04.07.536000
Hua-Ting Yao
1Department of Theoretical Chemistry, University of Vienna Währinger Straße 17, A-1090 Vienna, Austria
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  • For correspondence: htyao@tbi.univie.ac.at studla@bioinf.uni-leipzig.de
Ronny Lorenz
1Department of Theoretical Chemistry, University of Vienna Währinger Straße 17, A-1090 Vienna, Austria
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Ivo L. Hofacker
1Department of Theoretical Chemistry, University of Vienna Währinger Straße 17, A-1090 Vienna, Austria
2Research group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währingerstraße 29, A-1090, Vienna, Austria
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Peter F. Stadler
3Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, D-04107, Leipzig, Germany
4Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Interdisciplinary Center for Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv), and Leipzig Research Center for Civilization Diseases, Universität Leipzig, Augustusplatz 12, D-04107 Leipzig, Germany
5Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04109 Leipzig, Leipzig, Germany
1Department of Theoretical Chemistry, University of Vienna Währinger Straße 17, A-1090 Vienna, Austria
6Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Ciudad Universitaria, COL-111321 Bogotá, D.C., Colombia
7Santa Fe Institute, 1399 Hyde Park Rd., NM87501 Santa Fe, USA
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  • For correspondence: htyao@tbi.univie.ac.at studla@bioinf.uni-leipzig.de
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Abstract

Background RNA features a highly negatively charged phosphate backbone that attracts a of cloud counter-ions that reduce the electrostatic repulsion in a concentration dependent manner. Ion concentrations thus have a large influence on folding and stability of RNA structures. Despite their well-documented effects, salt effects are not handled by currently available secondary stucture prediction algorithms. Combining Debye-Hückel potentials for line charges and Manning’s counter-ion condensation theory, Einert et al. [Biophys. J. 100: 2745-2753 (2011)] modeled the energetic effects contributions monovalent cations on loops and helices.

Results The model of Einert et al. is adapted to match the structure of the dynamic programming recursion of RNA secondary structure prediction algorithms. An empirical term describing the dependence salt dependence of the duplex initiation energy is added to improve co-folding predictions for two or more RNA strands. The slightly modified model is implemented in the ViennaRNA package in such way that only the energy parameters but not the algorithmic structure is affected. A comparison with data from the literature show that predicted free energies and melting temperatures are in reasonable agreement with experiments.

Conclusion The new feature in the ViennaRNA package makes it possible to study effects of salt concentrations on RNA folding in a systematic manner. Strictly speaking, the model pertains only to mono-valent cations, and thus covers the most important parameter, i.e., the NaCl concentration. It remains a question for future research to what extent unspecific effects of bi- and tri-valent cations can be approximated in a similar manner.

Availability Corrections for the concentration of monovalent cations are available in the ViennaRNA package starting from version 2.6.0.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 08, 2023.
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Salt corrections for RNA secondary structures in the ViennaRNA package
Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
bioRxiv 2023.04.07.536000; doi: https://doi.org/10.1101/2023.04.07.536000
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Salt corrections for RNA secondary structures in the ViennaRNA package
Hua-Ting Yao, Ronny Lorenz, Ivo L. Hofacker, Peter F. Stadler
bioRxiv 2023.04.07.536000; doi: https://doi.org/10.1101/2023.04.07.536000

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