Analysis of Global Conformational Transitions in Ribozymes

The nucleolytic ribozymes are small, autonomously folding RNA species that require metal ions to adopt their active conformations. Three of these ribozymes contain one or more helical junctions, that act as key architectural elements in the structures. A combination of comparative gel electrophoresis and fluorescence resonance energy transfer (FRET) can be used to analyze the global conformation in solution, and to study the ion-induced folding processes. The FRET approach can also be extended into the time domain to analyze conformational equilibria, and increasingly to the single-molecule level.