Document Detail


Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference.
MedLine Citation:
PMID:  22913637     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Pablo Cordero; Wipapat Kladwang; Christopher C VanLang; Rhiju Das
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2012-08-29
Journal Detail:
Title:  Biochemistry     Volume:  51     ISSN:  1520-4995     ISO Abbreviation:  Biochemistry     Publication Date:  2012 Sep 
Date Detail:
Created Date:  2012-09-21     Completed Date:  2012-12-04     Revised Date:  2014-06-06    
Medline Journal Info:
Nlm Unique ID:  0370623     Medline TA:  Biochemistry     Country:  United States    
Other Details:
Languages:  eng     Pagination:  7037-9     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
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:
R01 GM102519/GM/NIGMS NIH HHS; R01 GM102519/GM/NIGMS NIH HHS; T32 HG000044/HG/NHGRI NIH HHS; T32 HG000044/HG/NHGRI NIH HHS
Chemical
Reg. No./Substance:
0/RNA, Bacterial; 0/Sulfuric Acid Esters; JW5CW40Z50/dimethyl sulfate
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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