Use of Fluorescence Spectroscopy to Elucidate RNA Folding Pathways

Philip C. Bevilacqua1, Douglas H. Turner2

1 The Pennsylvania State University, University Park, Pennsylvania, 2 University of Rochester, Rochester, New York
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 11.8
DOI:  10.1002/0471142700.nc1108s09
Online Posting Date:  August, 2002
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This overview unit discusses fluorescence spectroscopy as a tool for studying RNA folding. Ribozymes and oligonucleotides can be labeled with a fluorescent probe and analyzed to give information about both slow and fast kinetic processes with real‐time data acquisition. The unit discusses the advantages and disadvantages of various pendant probes and nucleotide analogs, the analytical methods that can be used, instrument setup, control experiments, and a variety of kinetic experiments that can be performed, such as determination of rate constants.

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Table of Contents

  • Preparation of Fluorescently Labeled RNA
  • Measuring Change in Fluorescence
  • Conclusion
  • Tables
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Literature Cited

Literature Cited
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Internet Resources
  ChemGenes site with catalog of precursors for synthesis of nucleic acids with fluorescent bases.
  Dharmacon Research site with catalog offering synthesis of labeled nucleic acids.
  Glen Research site with catalog of precursors for synthesis of labeled nucleic acids.
  Molecular Probes site with catalog and technical information for fluorophores.
  TriLink BioTechnologies site with catalog of fluorescent nucleoside triphosphates.
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