| Hydroxyl-radical footprinting to probe equilibrium changes in RNA tertiary structure. | |
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MedLine Citation:
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PMID: 20946763 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Hydroxyl-radical footprinting utilizes the ability of a highly reactive species to nonspecifically cleave the solvent accessible regions of a nucleic acid backbone. Thus, changes in a nucleic acids structure can be probed either as a function of time or of a reagent's concentration. When combined with techniques that allow single nucleotide resolution of the resulting fragments, footprinting experiments provide richly detailed information about local changes in tertiary structure of a nucleic acid accompanying its folding or ligand binding. In this chapter, we present two protocols of equilibrium hydroxyl-radical footprinting based on peroxidative and oxidative Fenton chemistry and discuss how to adjust the Fenton reagent concentrations for a specific experimental condition. We also discuss the choice of the techniques to separate the reaction products and specifics of the data analysis for equilibrium footprinting experiments. Protocols addressing the use of peroxidative Fenton chemistry for time-resolved studies have been published [Schlatterer and Brenowitz, 2009. Methods; Shcherbakova and Brenowitz, 2008. Nat. Protoc.3(2), 288-302; Shcherbakova et al., 2006. Nucleic Acids Res.34(6), e48; Shcherbakova et al., 2007. Methods Cell Biol.84, 589-615]. |
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Authors:
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Inna Shcherbakova; Somdeb Mitra |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural Date: 2009-11-17 |
Journal Detail:
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Title: Methods in enzymology Volume: 468 ISSN: 1557-7988 ISO Abbreviation: Meth. Enzymol. Publication Date: 2009 |
Date Detail:
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Created Date: 2010-10-15 Completed Date: 2011-01-26 Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 0212271 Medline TA: Methods Enzymol Country: United States |
Other Details:
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Languages: eng Pagination: 31-46 Citation Subset: IM |
Copyright Information:
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Copyright © 2009 Elsevier Inc. All rights reserved. |
Affiliation:
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Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Hydrogen Peroxide
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chemistry Hydroxyl Radical / chemistry* Iron / chemistry Nucleic Acid Conformation RNA / chemistry* |
| Grant Support | |
ID/Acronym/Agency:
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R01-GM085130/GM/NIGMS NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/Fenton's reagent; 3352-57-6/Hydroxyl Radical; 63231-63-0/RNA; 7439-89-6/Iron; 7722-84-1/Hydrogen Peroxide |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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