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  Home > JCE Print > Journal of Chemical Education > Issues > 2008  > May  >
In the Laboratory
Fluorescence Spectroscopy of tRNAPhe Y Base in the Presence of Mg2+ and Small Molecule Ligands
Sarah R. Kirk, Todd P. Silverstein, and Karen L. McFarlane Holman
Department of Chemistry, Willamette University, Salem, OR 97301
Cover
May 2008
Vol. 85 No. 5
p. 678

Abstract
This laboratory project is one component of a semester-long advanced biochemistry laboratory course that uses several complementary techniques to study tRNAPhe conformational changes induced by ligand binding. In this article we describe a set of experiments in which students use fluorescence spectroscopy to study tRNAPhe structure. Both intrinsic (Y Base) and extrinsic (ethidium bromide) fluorescence probes are monitored. Ligands (e.g., spermine, neomycin B, magnesium) are titrated into tRNAPhe solution and changes in fluorescence intensity are monitored. Students fit the data to hyperbolic saturation curves to determine ligand-binding equilibrium constants and draw conclusions on how different binding modes affect tRNAPhe tertiary structure.
Supplement
Detailed student manual; Instructor notes
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Citation
Kirk, Sarah R.; Silverstein, Todd P.; Holman, Karen L. McFarlane. J. Chem. Educ. 2008, 85, 678.
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Keywords
Biochemistry; Bioinorganic Chemistry; Bioorganic Chemistry; Biophysical Chemistry; Fluorescence Spectroscopy; Hands-On Learning / Manipulatives; Laboratory Instruction; Nucleic Acids / DNA / RNA; Upper-Division Undergraduate
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History
Created:
Last Updated:
3/25/2008
3/28/2008
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Experiments, laboratory exercises, lecture demonstrations, and other descriptions of the use of chemicals, apparatus, instruments, computers, and computer interfaces are presented in the Journal of Chemical Education as illustrative of new or improved ideas or concepts in chemistry instruction and are directed at qualified teachers. Although every effort is made to assure and encourage safe practices and safe use of chemicals, the Journal of Chemical Education cannot assume responsibility for uses made of its published materials. Many chemicals are hazardous. Precautions for the safe use of hazardous chemicals and directions for their proper disposal are described in the Material Safety Data Sheets and on the labels. We strongly urge all those planning to use materials from our pages to make choices and to develop procedures for laboratory and classroom safety in accordance with local needs and situations.
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