| The mechanisms of RNA SHAPE chemistry. | |
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MedLine Citation:
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PMID: 22475022 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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The biological functions of RNA are ultimately governed by the local environment at each nucleotide. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry is a powerful approach for measuring nucleotide structure and dynamics in diverse biological environments. SHAPE reagents acylate the 2'-hydroxyl group at flexible nucleotides because unconstrained nucleotides preferentially sample rare conformations that enhance the nucleophilicity of the 2'-hydroxyl. The critical corollary is that some constrained nucleotides must be poised for efficient reaction at the 2'-hydroxyl group. To identify such nucleotides, we performed SHAPE on intact crystals of the Escherichia coli ribosome, monitored the reactivity of 1490 nucleotides in 16S rRNA, and examined those nucleotides that were hyper-reactive toward SHAPE and had well-defined crystallographic conformations. Analysis of these conformations revealed that 2'-hydroxyl reactivity is broadly facilitated by general base catalysis involving multiple RNA functional groups and by two specific orientations of the bridging 3'-phosphate group. Nucleotide analog studies confirmed the contributions of these mechanisms to SHAPE reactivity. These results provide a strong mechanistic explanation for the relationship between SHAPE reactivity and local RNA dynamics and will facilitate interpretation of SHAPE information in the many technologies that make use of this chemistry. |
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Authors:
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Jennifer L McGinnis; Jack A Dunkle; Jamie H D Cate; Kevin M Weeks |
Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S. Date: 2012-04-05 |
Journal Detail:
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Title: Journal of the American Chemical Society Volume: 134 ISSN: 1520-5126 ISO Abbreviation: J. Am. Chem. Soc. Publication Date: 2012 Apr |
Date Detail:
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Created Date: 2012-04-18 Completed Date: 2012-09-26 Revised Date: 2012-10-05 |
Medline Journal Info:
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Nlm Unique ID: 7503056 Medline TA: J Am Chem Soc Country: United States |
Other Details:
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Languages: eng Pagination: 6617-24 Citation Subset: IM |
Copyright Information:
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© 2012 American Chemical Society |
Affiliation:
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Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Acylation Hydroxyl Radical Nucleic Acid Conformation* RNA / chemistry RNA, Ribosomal / chemistry* |
| Grant Support | |
ID/Acronym/Agency:
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R01-GM65050/GM/NIGMS NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/RNA primers; 0/RNA, Ribosomal; 3352-57-6/Hydroxyl Radical; 63231-63-0/RNA |
| Comments/Corrections | |
Erratum In:
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J Am Chem Soc. 2012 Jul 25;134(29):12319 |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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