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Updated: Apr 20, 2026

Nanomanipulation of Single RNA Molecules by Optical Tweezers
Published on: August 20, 2014
SHAPE analysis of small RNAs and riboswitches
Greggory M Rice1, Steven Busan1, Fethullah Karabiber2
1Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, USA.
Abstract:
We describe structural analysis of small RNAs by SHAPE chemical probing. RNAs are treated with 1-methyl-7-nitroisatoic anhydride, a reagent that detects local nucleotide flexibility; and N-methylisatoic anhydride and 1-methyl-6-nitroisatoic anhydride, reagents which together detect higher-order and noncanonical interactions. Chemical adducts are quantified as stops during reverse transcriptase-mediated primer extension. Probing information can be used to infer conformational changes and ligand binding and to develop highly accurate models of RNA secondary structures.
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