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Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package

, , , and . Algorithms for Molecular Biology, 18 (1): 8 (July 2023)
DOI: 10.1186/s13015-023-00236-0

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.

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