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Harnessing eSHAPE for Fine-Tuned Structure Prediction and Insight Into Protein-RNA Recognition

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"Harnessing eSHAPE for Fine-Tuned Structure Prediction and Insight Into Protein-RNA Recognition"

RNA structure is critical for understanding RNA function and regulation. Traditional biophysical methods for studying RNA structure like X-ray crystallography and NMR spectroscopy are powerful techniques, but they are costly, time-consuming, and require tremendous amounts of RNA.

Chemical probing techniques, such as SHAPE (Selective 2’-hydroxyl acylation analyzed by primer extension) can be used to study RNA structure, but they require familiarity with RNA probing, RNA library preparation, sequencing, and bioinformatics.

eSHAPE is based on SHAPE-MaP (SHAPE-mutational profiling), where RNA is first probed in vitro using the chemical probing agent, NAI, and then prepared for RNA sequencing. Mutations in the cDNA, caused by NAI adducts in the RNA during reverse transcription, are counted and computed into SHAPE reactivities to indicate paired and unpaired bases of an RNA.

This application note from Eclipsebio shows how its eSHAPE services can identify RNA-binding proteins bound to RNA, and how single-nucleotide polymorphisms can alter the structure of an mRNA molecule.

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