RNA molecules fold back on themselves to form complex secondary and tertiary structures. Knowledge of the three-dimensional fold as well as the underlying dynamics is essential to understand sequence-function relationships in RNA. A novel technique, called SHAPE chemistry, has been created for determining RNA secondary structure. In this work, I expand the applications of SHAPE chemistry in two directions: calculating opening rates for slow moving nucleotides and analysis of RNA dynamics at nucleotide resolution. First, I use SHAPE to identify a novel class of slow-moving nucleotides and calculate their opening rates. The major mechanism is that certain C2[prime]-endo nucleotides have slow, seconds long, opening rates. Second, I find a strong correlation between SHAPE chemistry and molecular order as measured by 13C NMR relaxation experiments. This finding validates SHAPE as an adequate substitute for 13C NMR relaxation experiments, expanding nucleotide-resolution dynamics analysis to large RNAs, inaccessible to NMR methods. Finally, I develop a fast, fully automated modeling method to determine three-dimensional structures of RNAs. This method blends (1) SHAPE-derived secondary structure information; (2) biochemical experiments that yield high quality tertiary structure information with (3) a coarse-grained molecular dynamics refinement. It therefore does not require any prior assumptions about secondary or tertiary structure, establishing the foundation for modeling and refining large RNAs inaccessible to crystallography and NMR techniques
