ArticleBiochemistry2008
SHAPE analysis of long-range interactions reveals extensive and thermodynamically preferred misfolding in a fragile group I intron RNA.
Article in Biochemistry, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Modeling the structure and DAP5-binding site of the FGF-9 5'-UTR RNA utilized in cap-independent translation.RNA (New York, N.Y.) · 2024Article
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
- High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites.Nature communications · 2018Article
- Direct identification of base-paired RNA nucleotides by correlated chemical probing.RNA (New York, N.Y.) · 2017Article
- Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.Nature protocols · 2015Article
- Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.Nucleic acids research · 2015Article
- Computational analysis of RNA structures with chemical probing data.Methods (San Diego, Calif.) · 2015Review
- Long-range architecture in a viral RNA genome.Biochemistry · 2013Article
- Toward a molecular understanding of RNA remodeling by DEAD-box proteins.RNA biology · 2013Review
- Comparison of SIV and HIV-1 genomic RNA structures reveals impact of sequence evolution on conserved and non-conserved structural motifs.PLoS pathogens · 2013Article
- The mechanisms of RNA SHAPE chemistry.Journal of the American Chemical Society · 2012Article
- Article
- Exploring RNA structural codes with SHAPE chemistry.Accounts of chemical research · 2011Article
- A two-dimensional mutate-and-map strategy for non-coding RNA structure.Nature chemistry · 2011Article
- Mapping studies of the Peach latent mosaic viroid reveal novel structural features.Molecular plant pathology · 2011Article
- ATP-dependent roles of the DEAD-box protein Mss116p in group II intron splicing in vitro and in vivo.Journal of molecular biology · 2011Article
- A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA.RNA (New York, N.Y.) · 2011Article
- SHAPE-directed RNA secondary structure prediction.Methods (San Diego, Calif.) · 2010Review
- Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease.Journal of the American Chemical Society · 2010Article
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2 authors.
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Abstract
Most functional RNAs require proteins to facilitate formation of their active structures. In the case of the yeast bI3 group I intron, splicing requires binding by two proteins, the intron-encoded bI3 maturase and the nuclear encoded Mrs1. Here, we use selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry coupled with analysis of point mutants to map long-range interactions in this RNA. This analysis reveals two critical features of the free RNA state. First, the catalytic intron is separated from the flanking exons via a stable anchoring helix. This anchoring helix creates an autonomous structural domain for the intron and functions to prevent misfolding with the flanking exons. Second, the thermodynamically most stable structure for the free RNA is not consistent with the catalytically active conformation as phylogenetically conserved elements form stable, non-native structures. These results highlight a fragile bI3 RNA for which binding by protein cofactors functions to promote extensive secondary structure rearrangements that are an obligatory prerequisite for forming the catalytically active tertiary structure.
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