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| 2mg |
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| Targets |
NAI acylates the 2′-OH in RNA, labeling single-stranded or flexible regions more than folded regions according to the SHAPE methodology. This reactivity enables the determination of RNA secondary and tertiary structure at nucleotide resolution in live cells.
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| ln Vitro |
In vitro studies with NAI involve treating purified RNA or RNA in cell lysates with the reagent and analyzing the acylation pattern. The compound preferentially reacts with flexible, single-stranded regions of RNA, while structured regions are less reactive. The acylation products are detected by reverse transcription primer extension or sequencing.
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| ln Vivo |
NAI is not used as a therapeutic agent but as a research tool for RNA structure probing. In vivo activity refers to its ability to penetrate living cells and modify RNA structures directly within the cellular environment. The compound enables SHAPE-MaP experiments in live cells.
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| Enzyme Assay |
For non-cellular assays, NAI is used in cell-free RNA structure probing experiments. Purified RNA or RNA in cell lysates is incubated with NAI, and the acylation reaction is allowed to proceed. The modified RNA is then analyzed by reverse transcription and sequencing to identify reactive positions. The reactivity profile reflects the local flexibility and structure of the RNA.
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| Cell Assay |
In vitro cellular assays with NAI involve treating live cells with the compound, which penetrates the cell membrane and acylates RNA within the cellular environment. Following treatment, RNA is extracted, and the acylation pattern is analyzed by SHAPE-MaP (mutational profiling) or similar techniques. This allows the determination of RNA structure in its native cellular context.
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| Animal Protocol |
NAI is not used in animal experiments as a therapeutic agent. It is a research reagent for RNA structure analysis. In some experimental settings, animals may be administered NAI for tissue RNA structure probing followed by ex vivo analysis, but this is not a standard application. The compound’s cell permeability makes it suitable for live-cell studies.
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| ADME/Pharmacokinetics |
NAI has a molecular weight of 187.20 and a molecular formula of C₁₀H₉N₃O. It is soluble in DMSO and is typically stored at -20°C. The compound is stable under recommended storage conditions. Its small size and cell permeability enable efficient cellular uptake for live-cell RNA structure studies.
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| Toxicity/Toxicokinetics |
NAI is a chemical reagent and is not intended for therapeutic use. Toxicity data are limited as it is used at low concentrations for RNA labeling. Standard laboratory safety precautions should be followed when handling the compound. It may cause skin, eye, and respiratory irritation as with many chemical reagents.
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| References |
Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, Chang HY. RNA SHAPE analysis in living cells. Nat Chem Biol. 2013 Jan;9(1):18-20. doi: 10.1038/nchembio.1131. Epub 2012 Nov 25. PubMed PMID: 23178934; PubMed Central PMCID: PMC3706714.
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| Additional Infomation |
NAI is a widely used reagent for RNA SHAPE probing. It enables the determination of RNA secondary and tertiary structure at nucleotide resolution in live cells. The compound is available from various commercial suppliers for research applications. NAI is particularly valuable for studying RNA structure-function relationships in their native cellular context.
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| Molecular Formula |
C10H9N3O
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|---|---|
| Molecular Weight |
187.2
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| Exact Mass |
187.075
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| CAS # |
1055970-47-2
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| Related CAS # |
1055970-47-2
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| PubChem CID |
66563654
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| Appearance |
Typically exists as solid at room temperature
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| LogP |
1.275
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| Hydrogen Bond Donor Count |
0
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| Hydrogen Bond Acceptor Count |
3
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| Rotatable Bond Count |
1
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| Heavy Atom Count |
14
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| Complexity |
219
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| Defined Atom Stereocenter Count |
0
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| SMILES |
CC1=C(C(N2C=CN=C2)=O)C=CC=N1
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| InChi Key |
OWQPEDNXDCVXJO-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C10H9N3O/c1-8-9(3-2-4-12-8)10(14)13-6-5-11-7-13/h2-7H,1H3 SMILES
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| Chemical Name |
Imidazol-1-yl-(2-methyl-pyridin-3-yl)-methanone
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| Synonyms |
NAI 2-Methylnicotinic acid imidazolide 2-Methylnicotinic acid imidazole
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| HS Tariff Code |
2934.99.9001
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| Storage |
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month |
| Shipping Condition |
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
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| Solubility (In Vitro) |
May dissolve in DMSO (in most cases), if not, try other solvents such as H2O, Ethanol, or DMF with a minute amount of products to avoid loss of samples
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| Solubility (In Vivo) |
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.
Injection Formulations
Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)(e.g. IP/IV/IM/SC) *Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution. Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil) Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals). View More
Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)] Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium) Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals). View More
Oral Formulation 3: Dissolved in PEG400 (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 5.3419 mL | 26.7094 mL | 53.4188 mL | |
| 5 mM | 1.0684 mL | 5.3419 mL | 10.6838 mL | |
| 10 mM | 0.5342 mL | 2.6709 mL | 5.3419 mL |
*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.
Calculation results
Working concentration： mg/mL；
Method for preparing DMSO stock solution： mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.
Method for preparing in vivo formulation:：Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O，mix and clarify.
(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
(2) Be sure to add the solvent(s) in order.
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