RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE).

By Edward J. Merino, K. Wilkinson, Jennifer L Coughlan, Kevin M. Weeks. Journal of the American Chemical Society, 2005

804 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/278b0bce7629520ae469737d9b7d3cd1e8dce4ac

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In Molecular Biology

Citations in the corpus

Automated 3D structure composition for large RNAs (2012, methodology): “The control reaction ( (cid:2) ) was subtracted from NMIA reaction (+) and SHAPE reactivities were processed as described (9).”
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. (2009, background): “29-Hydroxyl acylation analyzed by primer extension (SHAPE) chemistry can constrain both secondary structure and tertiary interactions ( Merino et al. 2005; Mortimer and Weeks 2007).”
DEAD-Box Helicases: Sensors, Regulators, and Effectors for Antiviral Defense (2020, background): “Additionally, in recent years, the application of RNA probing technologies such as SHAPE to viral RNAs is beginning to enable detailed analysis of secondary and tertiary structures that may be functionally relevant [30,91,92].”
Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. (2008, methodology): “Some recently developed methods like selective 29-hydroxyl acylation and primer extension (SHAPE) provide new possibilities for highthroughput measurements of RNA structures (Merino et al. 2005), but high-throughput methods capable of assessing structure in vivo still need to be developed.”
RNA design rules from a massive open laboratory (2014, methodology): “RNA sequences were prepared by in vitro transcription with T7 RNA polymerase from DNA templates encoding the sequence designs and probed with structure mapping based on Nmethylisatoic anhydride [SHAPE chemistry (17)] using 96-well protocols described previously (35).”
Accurate SHAPE-directed RNA structure determination (2009, methodology): “Local nucleotide flexibility can be measured at the vast majority of positions in any RNA by use of SHAPE (selective 2 -hydroxyl acylation analyzed by primer extension) chemistry (22, 23).”
RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) (2014, neutral): “O -adducts at conformationally flexible RNA nucleotides, both under simplified solution conditions 13,20 and in cells 15,16,21 .”
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures (2015, methodology): “If available, the SHAPE (selective 2 ′ -hydroxyl acylation analyzed by primer extension) Merino et al. 2005) experimental data were also Specifically, some nucleotides are restricted to be in loop regions (without forming base pairs with other nucleotides) because of their high SHAPE reactivity.”