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  Home > JCE Print > Journal of Chemical Education > Issues > 2008  > May  >
In the Laboratory
Metal-Catalyzed Cleavage of tRNAPhe
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. 676

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 assay metal-catalyzed hydrolysis of tRNAPhe using gel electrophoresis. tRNAPhe cleavage patterns are monitored in the presence of lead(II) and other metals cations. Small molecule ligands are also studied to determine their ability to enhance or inhibit lead(II)-catalyzed cleavage of tRNAPhe. Gel bands are quantified to determine ligand-binding equilibrium constants for the small molecule ligand–tRNAPhe adducts. By pooling class data from the metal and small molecule ligand experiments, students draw conclusions regarding how metal-catalyzed hydrolysis is affected by various parameters such as tRNAPhe structure, ligand charge, and inorganic chemistry of the metal ion complexes.
Supplement
Detailed student manual; Instructor notes
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Contents
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Citation
Kirk, Sarah R.; Silverstein, Todd P.; Holman, Karen L. McFarlane. J. Chem. Educ. 2008, 85, 676.
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Keywords
Biochemistry; Bioinorganic Chemistry; Bioorganic Chemistry; Electrophoresis; 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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