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Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

Article DOI: 10.3791/59021-v • 11:58 min • January 30th, 2019
January 30th, 2019 •
1, 2, 1
1Calibr, The Scripps Research Institute, 2Department of Integrative Structural and Computational Biology, The Scripps Research Institute

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Summary
Automatic Translation

Detailed protocols for both in vitro and in-cell selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) experiments to determine the secondary structure of pre-mRNA sequences of interest in the presence of an RNA-targeting small molecule are presented in this article.

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In Vitro In-cell SHAPE Small Molecule Induced Pre-mRNA Structural Changes RNA Sequences RNA Targeting Small Molecule Secondary Structure Nucleotide Dynamics RNA Template Radio Label Reverse Transcription Primers Gamma 32P ATP Reversed Transcription Primer Polynucleotide Kinase Desalting Column Centrifuge 2XTBE Urea Sample Buffer Acrylamide Gel Radioactivity Calcium-tungstate Phosphor Screen Imaging Instrument
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