| Size | Price | Stock | Qty |
|---|---|---|---|
| 5mg |
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| 10mg |
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| 100mg | |||
| Other Sizes |
| Targets |
NAI-N3 targets the 2'-hydroxyl group (2'-OH) in single-stranded RNA (ssRNA). It acylates this group, creating a covalent modification on the RNA. This chemical modification is used to probe RNA structure, as the reactivity of the 2'-OH is dependent on the local flexibility and dynamics of the RNA molecule.
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|---|---|
| ln Vitro |
Treatment of living cells with NAI-N3 using icSHAPE (In Vivo Click Selective 2-Hydroxy Acylation and Profiling Experiment) chemistry followed by selective chemical enrichment of NAI-N3 modified RNA yields increased confidence compared to similar RNA. Noise ratio employs deep sequencing approach [1].
In vitro, NAI-N3 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. The acylated RNA can then be purified and analyzed by next-generation sequencing to reveal RNA secondary structure information at a global scale. |
| ln Vivo |
In vivo, NAI-N3 is used for icSHAPE, which allows for the genome-wide profiling of RNA secondary structure in living cells. The compound is typically added to the cell culture medium, where it penetrates the cells and acylates the 2'-OH groups of RNA in their native cellular context.
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| Enzyme Assay |
The in vitro assay for NAI-N3 involves treating purified RNA or cells with the compound. For purified RNA, the compound is added to a solution containing the RNA of interest. After the acylation reaction, the RNA is purified, and the sites of modification are detected by primer extension or sequencing.
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| Cell Assay |
Cellular assays are performed by adding NAI-N3 directly to the culture medium of living cells. The cells are incubated for a period to allow the compound to penetrate and acylate the cellular RNA. The RNA is then extracted, and the sites of acylation are identified using a biotin-streptavidin pull-down and sequencing.
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| Animal Protocol |
In vivo, NAI-N3 is not administered to animals in the traditional sense. It is used in cell culture to study RNA structure within cells. The compound's effectiveness is evaluated by its ability to acylate RNA in a structure-dependent manner, which is then validated by sequencing and structural modeling.
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| ADME/Pharmacokinetics |
NAI-N3 has a molecular weight of 228.21 g/mol and a chemical formula of C10H8N6O. It is soluble in DMSO. As a small molecule, it can penetrate cell membranes to access cellular RNA. Its stability and reactivity in aqueous solutions are key to its function as a SHAPE probe.
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| Toxicity/Toxicokinetics |
NAI-N3 is a chemical reagent and is not intended for therapeutic use. Its toxicity is related to its reactivity, as it can covalently modify RNA. At the concentrations used for RNA probing, it is generally not cytotoxic. However, standard safety precautions should be followed.
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| References | |
| Additional Infomation |
NAI-N3 is a next-generation SHAPE reagent that enables the study of RNA structure in living cells. Its azide group allows for the enrichment and purification of modified RNA, making it a powerful tool for transcriptome-wide RNA structure analysis.
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| Molecular Formula |
C10H8N6O
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|---|---|
| Molecular Weight |
228.21
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| Exact Mass |
228.08
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| Elemental Analysis |
C, 52.63; H, 3.53; N, 36.83; O, 7.01
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| CAS # |
1612756-29-2
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| PubChem CID |
131704490
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| Appearance |
White to light yellow solid powder
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| LogP |
1.4
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| Hydrogen Bond Donor Count |
0
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| Hydrogen Bond Acceptor Count |
5
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| Rotatable Bond Count |
3
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| Heavy Atom Count |
17
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| Complexity |
327
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| Defined Atom Stereocenter Count |
0
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| InChi Key |
QPSQVTFTPHUCEH-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C10H8N6O/c11-15-14-6-9-8(2-1-3-13-9)10(17)16-5-4-12-7-16/h1-5,7H,6H2
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| Chemical Name |
[2-(azidomethyl)pyridin-3-yl]-imidazol-1-ylmethanone
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| Synonyms |
NAI-N3; NAIN3; NAI N3;
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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 Note: Please store this product in a sealed and protected environment, avoid exposure to moisture. |
| 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) |
DMSO : ~125 mg/mL (~547.74 mM)
H2O : ≥ 16.67 mg/mL (~73.05 mM) |
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| Solubility (In Vivo) |
Solubility in Formulation 1: ≥ 2.08 mg/mL (9.11 mM) (saturation unknown) in 10% DMSO + 90% (20% SBE-β-CD in Saline) (add these co-solvents sequentially from left to right, and one by one), clear solution.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 20.8 mg/mL clear DMSO stock solution to 900 μL of 20% SBE-β-CD physiological saline solution and mix evenly. Preparation of 20% SBE-β-CD in Saline (4°C，1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution. Solubility in Formulation 2: ≥ 2.08 mg/mL (9.11 mM) (saturation unknown) in 10% DMSO + 90% Corn Oil (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 20.8 mg/mL clear DMSO stock solution to 900 μL of corn oil and mix evenly. (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 4.3819 mL | 21.9096 mL | 43.8193 mL | |
| 5 mM | 0.8764 mL | 4.3819 mL | 8.7639 mL | |
| 10 mM | 0.4382 mL | 2.1910 mL | 4.3819 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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