Probing RNA Folding Pathways by RNA Fingerprinting

This unit provides protocols for using native polyacrylamide gel electrophoresis to distinguish folding and unfolding conformers of RNA. It is useful for studying conformers that can exchange in a period of minutes or seconds, and that are thus difficult to study by solution-based methods. Conformers that have been separated and immobilized in the gel matrix can be used to studying catalytic activity with or without being eluted from the gel. The method can be applied to a wide varied of catalytic RNAs and RNA-protein complexes.