Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference.
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ABSTRACT:
SUBMITTER: Cordero P
PROVIDER: S-EPMC3448840 | biostudies-literature | 2012 Sep
REPOSITORIES: biostudies-literature
Publications
Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference.
Cordero Pablo P Kladwang Wipapat W VanLang Christopher C CC Das Rhiju R
Biochemistry 20120829 36
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 ...[more]
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