Theory and simulations for RNA folding in mixtures of monovalent and divalent cations

Nguyen, Hung T.; Hori, Naoto; Thirumalai, D.

Abstract

RNA molecules require ions to fold. The problem of how ions of differing sizes and valences drive the folding of RNA molecules is unsolved. Here, we take a major step in its solution by creating a method, based on the theory of polyatomic liquids, to calculate the potential between divalent ions and the phosphate groups. The resulting model, accounting for inner and outer sphere coordination of Mg2+ and Ca2+ to phosphates, when used in coarse-grained molecular simulations, predicts folding free energies for a number of RNA molecules in the presence of both divalent and monovalent ions that are in excellent agreement with experiments. This work sets the stage for probing sequence and ion effects on DNA and synthetic polyelectrolytes.

Citation

Nguyen, H. T., Hori, N., & Thirumalai, D. (2019). Theory and simulations for RNA folding in mixtures of monovalent and divalent cations. Proceedings of the National Academy of Sciences, 116(42), 21022-21030. https://doi.org/10.1073/pnas.1911632116

• Journal Article Type: Article
• Acceptance Date: Sep 6, 2019
• Online Publication Date: Sep 30, 2019
• Publication Date: Oct 15, 2019
• Deposit Date: Sep 19, 2020
• Journal: Proceedings of the National Academy of Sciences
• Print ISSN: 0027-8424
• Electronic ISSN: 1091-6490
• Publisher: National Academy of Sciences
• Peer Reviewed: Peer Reviewed
• Volume: 116
• Issue: 42
• Pages: 21022-21030
• DOI: https://doi.org/10.1073/pnas.1911632116
• Keywords: Multidisciplinary
• Public URL: https://nottingham-repository.worktribe.com/output/4342499
• Publisher URL: https://www.pnas.org/content/116/42/21022