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Center for Nonlinear Studies |
The folding of a polymer chain into a specific molecular structure in an aqueous environment depends on a collection of non-covalent molecular interactions that stabilize particular configurations. For biological and biologically inspired polymer chains, intramolecular interactions between the monomeric subunits can induce a general ensemble of structures to form, but the stability and energetic favorability of these structures can then be affected by intermolecular interactions of the polymer with other surrounding molecules (i.e. solvent and cosolvents). These polymer-solution interactions affect the in situ behavior of several important classes of biomolecules, including ribonucleic acids (RNA). Using all-atom molecular dynamics simulations of a model RNA hairpin system in high concentrations of various cosolvent molecules (i.e. urea and neutral salts) we characterize the stability of the RNA hairpin as a function of the intermolecular interactions between RNA and solution. Our results reveal that RNA-cosolvent interactions specifically target particular chemical moieties in the RNA and induce significant shifts in the populations of different folded configurations. Additionally, our results describe a configuration-dependent preference for interactions with solvent and cosolvent molecules that recapitulates several decades of experimental research. Our results provide insight into critical molecular interactions that drive some of the most crucial structural behaviors of RNA in our cells. In addition, our methodology provides an important workflow for guiding future investigations into the effects of different aqueous solutions on the folding of RNA as well as other biological and biomimetic molecules.​
Host: Chris Neale