WARNING: This product is for research use only, not for human or veterinary use.
MedKoo CAT#: 464216
CAS#: 1612756-29-2
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.
MedKoo Cat#: 464216
Name: NAI-N3
CAS#: 1612756-29-2
Chemical Formula: C10H8N6O
Exact Mass: 228.076
Molecular Weight: 228.215
Elemental Analysis: C, 52.63; H, 3.53; N, 36.83; O, 7.01
Synonym: NAI-N3; NAIN3; NAI N3;
IUPAC/Chemical Name: (2-(azidomethyl)pyridin-3-yl)(1H-imidazol-1-yl)methanone
InChi Key: QPSQVTFTPHUCEH-UHFFFAOYSA-N
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
SMILES Code: [N-]=[N+]=NCC1=C(C=CC=N1)C(N2C=CN=C2)=O
Appearance: Solid powder
Purity: >98% (or refer to the Certificate of Analysis)
Shipping Condition: Shipped under ambient temperature as non-hazardous chemical. This product is stable enough for a few weeks during ordinary shipping and time spent in Customs.
Storage Condition: Dry, dark and at 0 - 4 C for short term (days to weeks) or -20 C for long term (months to years).
Solubility: To be determined
Shelf Life: >2 years if stored properly
Drug Formulation: to be determined
Stock Solution Storage: 0 - 4 C for short term (days to weeks), or -20 C for long term (months).
HS Tariff Code: 2934.99.9001
| Biological 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). |
| In vitro activity: | 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. Reference: Nat Protoc. 2016 Feb;11(2):273-90. https://pubmed.ncbi.nlm.nih.gov/26766114/ |
| In vivo activity: | 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. Reference: Nat Protoc. 2016 Feb;11(2):273-90. https://pubmed.ncbi.nlm.nih.gov/26766114/ |
| Solvent | Max Conc. mg/mL | Max Conc. mM | |
|---|---|---|---|
| Solubility | |||
| Ethanol | 16.67 | 73.05 | |
| DMSO | 250.0 | 1095.46 |
The following data is based on the product molecular weight 228.215 Batch specific molecular weights may vary from batch to batch due to the degree of hydration, which will affect the solvent volumes required to prepare stock solutions.
| Concentration / Solvent Volume / Mass | 1 mg | 5 mg | 10 mg |
|---|---|---|---|
| 1 mM | 1.15 mL | 5.76 mL | 11.51 mL |
| 5 mM | 0.23 mL | 1.15 mL | 2.3 mL |
| 10 mM | 0.12 mL | 0.58 mL | 1.15 mL |
| 50 mM | 0.02 mL | 0.12 mL | 0.23 mL |
| Formulation protocol: | 1. Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nat Protoc. 2016 Feb;11(2):273-90. doi: 10.1038/nprot.2016.011. Epub 2016 Jan 14. PMID: 26766114; PMCID: PMC4896316. |
| In vitro protocol: | 1. Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nat Protoc. 2016 Feb;11(2):273-90. doi: 10.1038/nprot.2016.011. Epub 2016 Jan 14. PMID: 26766114; PMCID: PMC4896316. |
| In vivo protocol: | 1. Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY. Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE. Nat Protoc. 2016 Feb;11(2):273-90. doi: 10.1038/nprot.2016.011. Epub 2016 Jan 14. PMID: 26766114; PMCID: PMC4896316. |
1: Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY. Transcriptome- wide interrogation of RNA secondary structure in living cells with icSHAPE. Nat Protoc. 2016 Feb;11(2):273-90. doi: 10.1038/nprot.2016.011. Epub 2016 Jan 14. PMID: 26766114; PMCID: PMC4896316.
