Salt corrections for RNA secondary structures in the ViennaRNA package

Abstract

AbstractBackgroundRNA 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, Einertet al. [Biophys. J.100: 2745-2753 (2011)] modeled the energetic effects contributions monovalent cations on loops and helices.ResultsThe model of Einertet 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 theViennaRNApackage 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.ConclusionThe new feature in theViennaRNApackage 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.AvailabilityCorrections for the concentration of monovalent cations are available in theViennaRNApackage starting from version 2.6.0.