Thermal Methods for the Analysis of RNA Folding Pathways

David E. Draper1, Yury V. Bukhman1, Thomas C. Gluick1

1 Johns Hopkins University, Baltimore, Maryland
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 11.3
DOI:  10.1002/0471142700.nc1103s02
Online Posting Date:  May, 2001
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Once a model of the secondary structure of an RNA has been deduced, thermal melting analysis can be used to determine whether the model accounts for all intramolecular interactions of the RNA, or whether noncanonical and tertiary interactions make the structure more stable than predicted, or link parts of the structure in unexpected ways. It is also useful to determine the pH, salt, and temperature ranges under which the RNA adopts a stably folded structure, or to analyze unfolding pathways. This unit discusses sample preparation, instrumentation, and theoretical background. It also provide a sample analysis of tRNA unfolding.

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Table of Contents

  • Experimental Considerations
  • Theoretical Background
  • Example Analysis: tRNA Unfolding
  • Experimental Tests of an Unfolding Pathway
  • Figures
  • Tables
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Literature Cited

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