RNA Folding pp 265-288 | Cite as

Detecting RNA Tertiary Folding by Sedimentation Velocity Analytical Ultracentrifugation

  • Somdeb Mitra
Part of the Methods in Molecular Biology book series (MIMB, volume 1086)


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 



The author wishes to express his gratitude to Dr. Ruben L. Gonzalez, Jr. for hosting him as a postdoctoral research scientist during the preparation of this manuscript, to Dr. Daniel MacDougall, Dr. Kelvin Caban, and Mr. Colin Kinz-Thompson for critically reading and commenting on the manuscript, to Dr. Michael Brenowitz for training him on AUC, and to Dr. Alain Laederach and Dr. Chunxia Chen for kindly providing the structural models of the Twort ribozyme. This work was supported partly by a Susan G. Komen for the Cure Postdoctoral Fellowship (PDF12231199) to the author and partly by a Research Project Grant (R01-GM 084288) from the National Institute of General Medicine and Sciences of the National Institute of Health to Dr. Ruben L. Gonzalez, Jr.


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Copyright information

© Springer Science+Business Media, LLC 2014

Authors and Affiliations

  • Somdeb Mitra
    • 1
  1. 1.Department of ChemistryColumbia UniversityNew YorkUSA

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