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Nucleic Acids Res. 2014 Feb;42(3):1947-58. doi: 10.1093/nar/gkt1051. Epub 2013 Nov 6.

Visualizing the ai5γ group IIB intron.

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Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA, Department of Chemistry, Yale University, New Haven, CT 06511, USA and Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.


It has become apparent that much of cellular metabolism is controlled by large well-folded noncoding RNA molecules. In addition to crystallographic approaches, computational methods are needed for visualizing the 3D structure of large RNAs. Here, we modeled the molecular structure of the ai5γ group IIB intron from yeast using the crystal structure of a bacterial group IIC homolog. This was accomplished by adapting strategies for homology and de novo modeling, and creating a new computational tool for RNA refinement. The resulting model was validated experimentally using a combination of structure-guided mutagenesis and RNA structure probing. The model provides major insights into the mechanism and regulation of splicing, such as the position of the branch-site before and after the second step of splicing, and the location of subdomains that control target specificity, underscoring the feasibility of modeling large functional RNA molecules.

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