Description
NAI-N3 is a probe for icSHAPE (in vivo click selective 2'-hydroxyl acylation and profiling experiment). It acylates the 2'-OH in ssRNA and enables RNA structure profiling in vivo and ex vivo for all four bases. NAI-N3 can be used for site-specific RNA acylation using the RAIL (RNA Acylation at Induced Loops) method or in Apta-Seq to discover new aptamers in selected pools.
Uses
NAI 1 is used in the process of visualizing the physical basis for molecular behaviours inside living cells. RNAs are central to biological regulation and this molecule aids in the first global view of RNA secondary structures in living cells for all four bases.
in vitro
In brief, the bifunctional NAI-N3 SHAPE reagent is used to label all RNAs inside living cells (or in vitro refolded RNA) to generate covalent modifications on targeted RNAs at single-nucleotide resolution. _x000D_
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Reference: Nat Protoc. 2016 Feb;11(2):273-90. https://pubmed.ncbi.nlm.nih.gov/26766114/
in vivo
This study has tested the NAI-N3 reagent in bacterial (Gram-negative Escherichia coli), yeast, insect and mammalian cells for SHAPE experiments. All of these systems proved to be amenable for icSHAPE modification and RNA structure determination. This study has successfully generated icSHAPE data from experiments in which the in vivo modification occurs at temperatures between 30 and 37 °C, to accommodate the specific culture temperatures. Thus, the procedure can be easily adapted to a wide variety of culture systems to allow transcriptome-wide RNA structure determination in most model systems._x000D_
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Reference: Nat Protoc. 2016 Feb;11(2):273-90. https://pubmed.ncbi.nlm.nih.gov/26766114/
target
NAI-N3 is a RNA acylation reagent that enables RNA purification. NAI-N3 is a dual-function SHAPE (selective 2-hydroxyl acylation and profiling experiment) probe (RNA structure probe and enrichment).
