This project focuses the ubiquitous ion atmosphere, which profoundly influences the overall folding of all complex RNAs. We have chosen to work with simple, structurally well-defined constructs to isolate electrostatic interactions involving the ion atmosphere to their basic core elements. This basic, comprehensive, and rich data is used to rigorously develop and test state-of-the-art electrostatic models and theories that can be applied for prediction and used as tools for design in more complicated RNA systems.
Using this reconstitution hypothesis, we propose to predict, in a “bottom-up” manner, the folding behavior of natural RNAs and RNA-protein complexes. The results will significantly advance our understanding, either providing strong evidence for the reconstitution hypothesis and demonstrating predictive power via multiple non-trivial tests, or identifying complexities in RNA and RNA/protein behavior that can be tested and incorporated into next-generation models.
