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

ABSTRACT: RNA molecules cannot fold in the absence of counterions. Experiments are typically performed in the presence of monovalent and divalent cations. How to treat the impact of a solution containing a mixture of both ion types on RNA folding has remained a challenging problem for decades. By exploiting the large concentration difference between divalent and monovalent ions used in experiments, we develop a theory based on the reference interaction site model (RISM), which allows us to treat divalent cations explicitly while keeping the implicit screening effect due to monovalent ions. Our theory captures both the inner shell and outer shell coordination of divalent cations to phosphate groups, which we demonstrate is crucial for an accurate calculation of RNA folding thermodynamics. The RISM th

SUBMITTER: Nguyen HT 

PROVIDER: S-EPMC6800359 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature