SHAPE Reagents

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SHAPE Reagents
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SHAPE Reagents for RNA structural Analysis

• SHAPE (Selective 2'-Hydroxyl Acylation and Primer
  Extension) reagents are used for the analysis of
  local nucleotide dynamics in RNA developed based
  on isatoic anhydride.
• SHAPE reagents selectively acylate the ribose
  2'-hydroxy group of the non-internally paired RNA
  backbone (sugar-phosphate backbone) to modify
  bases and to enable detection of unpaired bases
  by primer extension or by protection from
  exoribonuclease digestion.

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Unlike base-specific probes used similarly for
RNA conformational analysis, generalist probes
including SHAPE reagents react with the RNA
backbone, allowing simultaneous monitoring of all
nucleotides.
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TCI SHAPE Reagents

• TCI offers 6 products with different
  characteristics, including N-Methylisatoic
  Anhydride (Product No. M0743), which has been
  widely used as a SHAPE reagent.

Product No Name
M0743 N-Methylisatoic Anhydride
M3578 1-Methyl-7-nitroisatoic Anhydride
M3589 1-Methyl-6-nitroisatoic Anhydride
N1245 5-Nitroisatoic Anhydride
B0835 Benzoyl Cyanide
A0694 N-Acetylimidazole
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Products
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Characteristics of Each SHAPE Reagent
SHAPE Reagent Half-Life () Characteristics
N-Methylisatoic Anhydride ( NMIA) 430 sec. Widely used as a SHAPE reagent.
N-Methylisatoic Anhydride ( NMIA) 430 sec. Unsuitable for modification of intracellular RNA.1)
1-Methyl-7-nitroisatoic Anhydride ( 1M7) 14 sec. Widely used as a SHAPE reagent.
1-Methyl-7-nitroisatoic Anhydride ( 1M7) 14 sec. The nucleotide bias is low.
1-Methyl-7-nitroisatoic Anhydride ( 1M7) 14 sec. It tends to favor in vivo over in vitro use compared to other SHAPE reagents.2)
1-Methyl-6-nitroisatoic Anhydride ( 1M6) 31 sec. Similar to 1M7, it has high versatility and is suitable for cell-free assays.
1-Methyl-6-nitroisatoic Anhydride ( 1M6) 31 sec. It has faster reactivity than NMIA.3)
5-Nitroisatoic Anhydride ( 5NIA) 100 sec. Suitable for the modification of RNA in living cells.2)
Benzoyl Cyanide ( BzCN) 0.25 sec. Useful for tracking RNA folding in seconds due to its fast reaction rate and rapid inactivation by hydrolysis.4)
N-Acetylimidazole ( AcIm) 3-30 min. Produces minimal acetyl adducts.
N-Acetylimidazole ( AcIm) 3-30 min. It has been reported that the reaction rate is faster than 2-Methylnicotinic Acid Imidazolide ( NAI).
N-Acetylimidazole ( AcIm) 3-30 min. More suitable for structural profiling of long RNAs in nanoSHAPE than other SHAPE probes.5,6)
Measurement conditions vary according to the
reported paper.