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.
%0 Journal Article
%1 yao2023monovalent
%A Yao, Hua-Ting
%A Lorenz, Ronny
%A Hofacker, Ivo L.
%A Stadler, Peter F.
%D 2023
%J Algorithms for Molecular Biology
%K imported
%N 1
%P 8
%R 10.1186/s13015-023-00236-0
%T Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package
%U https://doi.org/10.1186/s13015-023-00236-0
%V 18
%X 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.
@article{yao2023monovalent,
abstract = {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.},
added-at = {2024-10-02T13:52:45.000+0200},
author = {Yao, Hua-Ting and Lorenz, Ronny and Hofacker, Ivo L. and Stadler, Peter F.},
biburl = {https://puma.scadsai.uni-leipzig.de/bibtex/2c738b170d91a1be245d772799a1fe478/scadsfct},
doi = {10.1186/s13015-023-00236-0},
interhash = {671ec8222866cc25e7b96f08bff19997},
intrahash = {c738b170d91a1be245d772799a1fe478},
issn = {1748-7188},
journal = {Algorithms for Molecular Biology},
keywords = {imported},
month = jul,
number = 1,
pages = 8,
timestamp = {2024-10-02T13:52:45.000+0200},
title = {Mono-valent salt corrections for {RNA} secondary structures in the {ViennaRNA} package},
url = {https://doi.org/10.1186/s13015-023-00236-0},
volume = 18,
year = 2023
}
