The solvent-protected core of the hairpin ribozyme-substrate complex

Hydroxyl radical footprinting was used to define the interface between the two domains of the hairpin ribozyme responsible for the interaction with the substrate. Results reveal the presence of a solvent-protected core associated with the internal loops of the enzyme-substrate complex. The experimental protocol used in the investigation can be utilized in the investigation of the requirements in the interaction between the two domains and the analysis of the interactions between them.