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

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 pre

SUBMITTER: Yao HT 

PROVIDER: S-EPMC10386259 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature