Titel
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package
Autor*in
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Abstract
Background: RNA features a highly negatively charged phosphate backbone that attracts a cloud of 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 consistently by currently available secondary structure 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 contributions of 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 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.
Stichwort
RNA secondary structureSalt concentrationDebye-Hückel potential
Objekt-Typ
Sprache
Englisch [eng]
Persistent identifier
phaidra.univie.ac.at/o:2065406
Erschienen in
Titel
Algorithms for Molecular Biology
Band
18
ISSN
1748-7188
Erscheinungsdatum
2023
Publication
Springer Science and Business Media LLC
Fördergeber
Erscheinungsdatum
2023
Zugänglichkeit
Rechte
Rechteangabe
© The Author(s) 2023
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