Post-transcriptional gene regulation is accomplished through the actions of RNA binding proteins and structured RNAs that control RNA stability, splicing, modification, localization, and translation. Manipulation of these processes is increasingly being employed to develop therapeutic and diagnostic applications. However, many of these applications will require developing quantitative, predictive biophysical models of how RNA binding proteins and structured RNAs function. To this point, the lack of approaches for high-throughput characterization of such systems has greatly hampered progress toward this goal. I am aiming to overcome these limitations by applying high-throughput methods to make millions of biophysical measurements in parallel. Using these methods, I am interested in 1) probing the folding and catalysis of large functional RNAs to better understand how RNA can be used to form complex molecular machines and 2) examining the sequence specificity of RNA and DNA binding proteins.