Journal
BIOCHEMISTRY
Volume 53, Issue 43, Pages 6825-6833Publisher
AMER CHEMICAL SOC
DOI: 10.1021/bi501218g
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Funding
- National Science Foundation [MCB-1121024]
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [1121024] Funding Source: National Science Foundation
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We introduce a melded chemical and computational approach for probing and modeling higher-order intramolecular tertiary interactions in RNA. 2'-Hydroxyl molecular interference (HMX) identifies nucleotides in highly packed regions of an RNA by exploiting the ability of bulky adducts at the 2'-hydroxyl position to disrupt overall RNA structure. HMX was found to be exceptionally selective for quantitative detection of higher-order and tertiary interactions. When incorporated as experimental constraints in discrete molecular dynamics simulations, HMX information yielded accurate three-dimensional models, emphasizing the power of molecular interference to guide RNA tertiary structure analysis and fold refinement. In the case of a large, multidomain RNA, the Tetrahymena group I intron, HMX identified multiple distinct sets of tertiary structure interaction groups in a single, concise experiment.
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