| Size | Price | Stock | Qty |
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| 1mg |
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| 5mg |
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| 10mg |
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| Targets |
RNA (psoralen-reactive sites) and proteins (primary amines). The psoralen moiety is a photoactivatable group that intercalates into RNA and upon UV-A irradiation (365 nm) covalently crosslinks to uridine bases. The NHS ester group reacts spontaneously with primary amines (-NH2) on lysine residues and N-termini of proteins. The dual functionality allows it to form covalent crosslinks between RNA and any interacting protein.
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| ln Vitro |
AMT-NHS is not a drug with an IC50; it's a chemical crosslinker. Its activity is its ability to form covalent crosslinks between RNA and proteins in situ. In live yeast cells, it penetrates the cell wall and membrane and crosslinks Cbf5 (a protein) to H/ACA snoRNAs with high specificity. It can also induce different cross-linking patterns and target both single-stranded and double-stranded regions of RNA.
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| ln Vivo |
The in vivo activity of AMT-NHS is demonstrated by its ability to capture RNA-protein interactions in live cells. When added to a culture of live yeast cells (or other organisms like C. elegans), it permeates the cells. The cells are then irradiated with 365 nm UV-A light to activate the psoralen moiety, crosslinking RNA-protein complexes. The crosslinked complexes can be purified and analyzed to identify interacting partners, revealing the interactome.
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| Enzyme Assay |
The reaction is performed by incubating a solution of AMT-NHS with purified RNA and protein (or cell lysate) in a buffer at pH 7.2-9.0. First, the NHS ester reacts with primary amines on proteins. The sample is then exposed to long-wave UV-A light (~365 nm), which activates the psoralen moiety to covalently bind to RNA. The efficiency of crosslinking can be verified by gel shift assays where the RNA-protein complex appears at a higher molecular weight than the free RNA or protein.
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| Cell Assay |
The ability of AMT-NHS to crosslink RNA-protein interactions in living cells is its primary in vitro/in situ assay. Live cells (e.g., HEK293T, yeast) are treated with AMT-NHS. After a brief incubation period to allow the NHS-ester to react with cellular proteins, the cells are irradiated with UV-A light (e.g., using a 365 nm lamp) for a few minutes on ice to induce the RNA crosslinking. Cells are then lysed, and crosslinked RNA-protein complexes are purified for downstream analysis (e.g., RT-qPCR, sequencing).
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| Animal Protocol |
In vivo experiments are typically performed by treating live model organisms like C. elegans. Worms grown on standard plates are washed and resuspended in a solution containing AMT-NHS. After a short incubation to allow the compound to penetrate, the worms are exposed to UV-A light to trigger crosslinking. The worms are then collected and lysed. The crosslinked RNA-protein complexes are then processed to identify the RNAs associated with specific proteins or vice versa.
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| ADME/Pharmacokinetics |
AMT-NHS is a small molecule crosslinker. For in vivo experiments in cells or organisms, it is typically dissolved in an organic solvent like DMSO to make a stock solution, which is then diluted into an aqueous buffer (e.g., PBS) immediately before use. It is cell-permeable and stable enough for short-term incubations. The specific pharmacokinetics (PK) are not characterized, as it is a chemical probe not intended for systemic administration as a therapeutic.
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| Toxicity/Toxicokinetics |
As a reactive crosslinker, AMT-NHS is toxic and a potential skin and eye irritant. It should be handled with extreme care in a fume hood using appropriate personal protective equipment (PPE). The NHS ester is reactive and can hydrolyze. The compound is light-sensitive due to the psoralen moiety, which can be activated by ambient light, so it must be stored in the dark. Long-term exposure to living organisms should be minimized and is typically done for short periods (e.g., 1-2 hours).
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| References |
[1]. Han Y, et al. Development of an RNA-protein crosslinker to capture protein interactions with diverse RNA structures in cells. RNA. 2022 Mar;28(3):390-399.
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| Additional Infomation |
AMT-NHS is a research-use-only chemical probe for studying RNA-protein interactions. It was developed to overcome the limitations of crosslinkers that only target one type of molecule. Its unique structure allows for the simultaneous and covalent capture of RNA-protein complexes directly in their native cellular environment, providing a snapshot of the interactome. It can be used in various applications, including mapping RNA-binding proteins (RBPs) and studying non-coding RNA function. It is not a drug or a drug candidate.
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| Exact Mass |
443.104
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|---|---|
| CAS # |
2925268-86-4
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| PubChem CID |
164887507
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| Appearance |
White to off-white solid powder
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| Hydrogen Bond Donor Count |
0
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| Rotatable Bond Count |
7
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| Heavy Atom Count |
31
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| Complexity |
796
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| Defined Atom Stereocenter Count |
0
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| SMILES |
CC1=CC(=O)OC2=C(C3=C(C=C12)C(=C(O3)C)CSCCC(=O)ON4C(=O)CCC4=O)C
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| InChi Key |
OOLVYUSWNMDHMP-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C22H21NO7S/c1-11-8-20(27)29-21-12(2)22-15(9-14(11)21)16(13(3)28-22)10-31-7-6-19(26)30-23-17(24)4-5-18(23)25/h8-9H,4-7,10H2,1-3H3
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| Chemical Name |
(2,5-dioxopyrrolidin-1-yl) 3-[(2,5,9-trimethyl-7-oxofuro[3,2-g]chromen-3-yl)methylsulfanyl]propanoate
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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) |
DMSO: 25 mg/mL (56.37 mM)
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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.) |
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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