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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.
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.
TCI offers 6 products with different characteristics, including N-Methylisatoic Anhydride (Product No. M0743), which has been widely used as a SHAPE reagent.
Products
Characteristics of Each SHAPE Reagent
| SHAPE Reagent | Half-Life (*) | Characteristics |
|---|---|---|
| N-Methylisatoic Anhydride (= NMIA) | 430 sec. | Widely used as a SHAPE reagent. Unsuitable for modification of intracellular RNA.1) |
| 1-Methyl-7-nitroisatoic Anhydride (= 1M7) | 14 sec. | Widely used as a SHAPE reagent. The nucleotide bias is low. 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. 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. It has been reported that the reaction rate is faster than 2-Methylnicotinic Acid Imidazolide (= NAI). More suitable for structural profiling of long RNAs in nanoSHAPE than other SHAPE probes.5,6) |
* Measurement conditions vary according to the reported paper.
Related Product Category Pages
TCI also offers nucleobase-specific probes and nucleoside triphosphates.
References
- 1) RNA Structure Analysis at Single Nucleotide Resolution by Selective 2'-Hydroxyl Acylation and Primer Extension (SHAPE)
- 2) Guidelines for SHAPE Reagent Choice and Detection Strategy for RNA Structure Probing Studies
- 3) Fingerprinting Noncanonical and Tertiary RNA Structures by Differential SHAPE Reactivity
- 4) Time-Resolved RNA SHAPE Chemistry
- 5) Direct detection of RNA modifications and structure using single-molecule nanopore sequencing
- 6) Polyacetate and Polycarbonate RNA: Acylating Reagents and Properties
