A new method to monitor the rate of conformational transitions in RNA

Biophysical analysis of nucleic acids

This overview unit provides a thorough overview of biophysical methods used for structure analysis, including X-ray diffraction, nuclear magnetic resonance, optical spectroscopy, theoretical and computational methods, and single-molecule methods. Advantages and disadvantages of the methods are compared.

Rapid magnesium chelation as a method to study real-time tertiary unfolding of RNA

This unit describes a method to measure the unfolding of RNA tertiary structure on a millisecond time scale. A stopped-flow spectrophotometer is used to measure the rate of unfolding induced by the addition of EDTA to an RNA whose tertiary structure has been stabilized in the presence of magnesium ions. Using this methodology, rate constants for unfolding of tertiary or secondary structure can be obtained over a range of temperatures, and these values can be used to construct Arrhenius and Eyring plots, from which activation energy, Arrhenius pre-exponential factor, and enthalpy and entropy of activation can be obtained. These data provide information about the energy of the transition state and the energy barriers between secondary and tertiary structure, which is necessary for predicting RNA tertiary structure from secondary structure.

RNA folding pathways

A general overview of the questions and problems in RNA folding is presented. Topics include the differences in the folding problems/questions that apply to RNA versus proteins, methods for determination of final structures, folding versus unfolding, resolution of space and time, and conformational switching.