The mechanisms and driving forces of the assembly of RNA tertiary structure are a topic of much current interest. In several systems, including our own work in the docking transition of the hairpin ribozyme, intramolecular RNA tertiary folding has been converted into an intermolecular binding event, allowing the full power of contemporary biophysical techniques to be brought to bear on the analysis. We review the use of three such methods: circular dichroism to isolate the binding of multivalent cations coupled to tertiary assembly, surface plasmon resonance to determine the rates of association and dissociation, and isothermal titration calorimetry to dissect the thermodynamic contributions to RNA assembly events. We pay particular attention to practical aspects of these studies, such as careful preparation of samples with fixed free concentrations of cations in order to avoid errors due to ion depletion effects that are common in RNA systems. Examples of applications from our own work with the hairpin ribozyme are shown. Distinctions among the data handling procedures for the various techniques used and solution conditions encountered are also discussed.
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