| Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference. | |
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MedLine Citation:
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PMID: 22913637 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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For decades, dimethyl sulfate (DMS) mapping has informed manual modeling of RNA structure in vitro and in vivo. Here, we incorporate DMS data into automated secondary structure inference using an energy minimization framework developed for 2'-OH acylation (SHAPE) mapping. On six noncoding RNAs with crystallographic models, DMS-guided modeling achieves overall false negative and false discovery rates of 9.5% and 11.6%, respectively, comparable to or better than those of SHAPE-guided modeling, and bootstrapping provides straightforward confidence estimates. Integrating DMS-SHAPE data and including 1-cyclohexyl(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate (CMCT) reactivities provide small additional improvements. These results establish DMS mapping, an already routine technique, as a quantitative tool for unbiased RNA secondary structure modeling. |
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Authors:
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Pablo Cordero; Wipapat Kladwang; Christopher C VanLang; Rhiju Das |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't Date: 2012-08-29 |
Journal Detail:
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Title: Biochemistry Volume: 51 ISSN: 1520-4995 ISO Abbreviation: Biochemistry Publication Date: 2012 Sep |
Date Detail:
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Created Date: 2012-09-21 Completed Date: 2012-12-04 Revised Date: 2013-04-16 |
Medline Journal Info:
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Nlm Unique ID: 0370623 Medline TA: Biochemistry Country: United States |
Other Details:
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Languages: eng Pagination: 7037-9 Citation Subset: IM |
Affiliation:
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Department of Biomedical Informatics, Stanford University, Stanford, CA 94305, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Acylation Automation Base Sequence Computational Biology / methods* Models, Molecular Nucleic Acid Conformation / drug effects* RNA, Bacterial / chemistry*, genetics Sulfuric Acid Esters / pharmacology* |
| Grant Support | |
ID/Acronym/Agency:
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R01 GM102519/GM/NIGMS NIH HHS; R01 GM102519/GM/NIGMS NIH HHS; T32 HG000044/HG/NHGRI NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/RNA, Bacterial; 0/Sulfuric Acid Esters; JW5CW40Z50/dimethyl sulfate |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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