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RNA Folding

Volume 1086 of the series Methods in Molecular Biology pp 265-288

Date:

Detecting RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation

  • Somdeb MitraAffiliated withDepartment of Chemistry, Columbia University

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Abstract

Analytical Ultracentrifugation (AUC) is a highly sensitive technique for detecting global conformational features of biological molecules and molecular interactions in solution. When operated in a sedimentation velocity (SV) recording mode, it reports precisely on the hydrodynamic properties of a molecule, including its sedimentation and diffusion coefficients, which can be used to calculate its hydrated radius, as well as, to estimate its global shape. This chapter describes the application of SV-AUC to the detection of global conformational changes accompanying equilibrium counterion induced tertiary folding of structured RNA molecules. A brief theoretical background is provided at the beginning, aimed at familiarizing the readers with the operational principle of the technique; then, a detailed set of instructions is provided on how to design, conduct, and analyze the data from an equilibrium RNA folding experiment, using SV-AUC.

Key words

RNA folding Counterion Analytical ultracentrifugation Sedimentation velocity Hydrodynamic measurements