| Size | Price | Stock | Qty |
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| 1mg |
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| 5mg |
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| Other Sizes |
Purity: ≥98%
| Targets |
PhenDC3 potently inhibited the helicase activity of FANCJ on a unimolecular G4 DNA substrate (Poly(A) Zic1) in a concentration-dependent manner, with an IC50 value of 0.37 ± 0.08 nM. This inhibition was highly specific to G4 DNA structures, as PhenDC3 had little to no effect on FANCJ's unwinding of a forked duplex DNA substrate. [1]
The inhibitory potency of PhenDC3 on FANCJ helicase activity was strongly dependent on the topology of the G4 substrate. The IC50 value for inhibition on the unimolecular G4 substrate was approximately 150-fold lower (more potent) than for the tetramolecular G4 substrate (IC50 = 65 ± 6 nM) and approximately 875-fold lower than for the bimolecular G4 substrate (IC50 = 370 ± 60 nM). [1] PhenDC3 also inhibited the helicase activity of DinG, another Fe-S helicase, on tetramolecular and bimolecular G4 DNA substrates, with IC50 values of 50 ± 10 nM and 85 ± 10 nM, respectively. [1] In G4 Fluorescent Intercalator Displacement (G4-FID) assays, PhenDC3 efficiently displaced thiazole orange (TO) from unimolecular G4 DNA substrates (3'-Poly(A) Zic1-G4 and 5'-Poly(A) Zic1-G4), demonstrating its ability to bind these structures. The binding to the bimolecular OX-1-G2' substrate was less efficient, as indicated by a higher DC50 value (concentration for 50% TO displacement). [1] |
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| ln Vitro |
While CEB1-WT remains very stable in WT cells, it rearranges in gaps when 10 μM Phen-DC3 triflate (Phen-DC3) is added. Significant stability of the c-Myc allele was seen following Phen-DC3 triflate treatment and PIF1. The CEB25-L111(T) array is stable in WT cells and stabilizes when Phen-DC3 triflate is added or PIF1 is removed. Moreover, it becomes extremely unstable when Phen-DC3 triflate or PIF1 are present. Both WT cells and PIF1-treated cells exhibit perfect stability of the CEB1 loop CEB25 allele [2].
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| Enzyme Assay |
Helicase Inhibition Assay: The inhibitory effect of PhenDC3 on DNA helicase activity was assessed using purified recombinant FANCJ or DinG proteins. Helicase reactions (20 µL) were performed under standard conditions with a 5'-³²P-labeled DNA substrate (0.25 nM). The G4 DNA substrates used were: unimolecular 5' Poly(A) Zic1-G4, tetramolecular TP-G4, and bimolecular OX-1-G2'. PhenDC3, dissolved in DMSO, was added to the reaction at increasing concentrations (ranging from 0 to 10 µM) and pre-incubated with the enzyme and substrate. The reaction was initiated by adding ATP and incubated at 30°C (for FANCJ) or 37°C (for DinG) for 15 minutes. Reactions were stopped, and products were resolved by native polyacrylamide gel electrophoresis. The percentage of DNA unwound was quantified, and IC50 values (the concentration of PhenDC3 required to inhibit 50% of the helicase activity) were calculated from dose-response curves. Control experiments with forked duplex DNA were performed to confirm the G4-specificity of the inhibition. [1]
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| Cell Assay |
G4-FID (Fluorescent Intercalator Displacement) Assay for G4 DNA Binding: The binding affinity of PhenDC3 for various G4 DNA topologies was evaluated using a G4-FID assay. First, pre-folded G4 DNA substrates (0.25 µM) were mixed with thiazole orange (TO, 0.50 µM) in a buffer containing 10 mM lithium cacodylate (pH 7.4) and 100 mM KCl, and the fluorescence spectrum was recorded (excitation 495 nm, emission measured between 510-750 nm). Then, increasing concentrations of PhenDC3 (from a 0.125 mM stock in DMSO) were added stepwise, with a 3-minute equilibration after each addition, followed by fluorescence measurement. The displacement of TO, indicated by a decrease in fluorescence, was calculated as: TO displacement (%) = 100 - [(FA / FA0) × 100], where FA is the fluorescence area after ligand addition and FA0 is the initial fluorescence area. The percentage of fluorescence variation was plotted against ligand concentration, and the DC50 value, the concentration needed to displace 50% of the TO, was determined by non-linear fitting of the displacement curve. [1]
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| References |
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| Additional Infomation |
PhenDC3 is a synthetic bisquinolinium compound known to specifically bind G-quadruplex (G4) DNA structures. In this study, it was used as a tool to probe the G4-unwinding activity of iron-sulfur cluster helicases like FANCJ and DinG. [1]
The extreme potency of PhenDC3 in inhibiting FANCJ on unimolecular G4 DNA (IC50 = 0.37 nM) compared to multi-stranded G4 structures highlights the importance of G4 topology in ligand-enzyme interactions. This suggests that PhenDC3 and related compounds could be valuable for dissecting the molecular specificity of G4-metabolizing enzymes. [1] |
| Molecular Formula |
C35H26F3N6O5S
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|---|---|
| Molecular Weight |
699.678356647491
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| Exact Mass |
848.115
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| CAS # |
929895-45-4
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| Related CAS # |
Phen-DC3;942936-75-6
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| PubChem CID |
131704505
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| Appearance |
White to light yellow solid powder
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| Hydrogen Bond Donor Count |
2
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| Hydrogen Bond Acceptor Count |
16
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| Rotatable Bond Count |
4
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| Heavy Atom Count |
58
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| Complexity |
1050
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| Defined Atom Stereocenter Count |
0
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| SMILES |
C[N+]1=CC(=CC2=CC=CC=C21)NC(=O)C3=NC4=C(C=CC5=C4N=C(C=C5)C(=O)NC6=CC7=CC=CC=C7[N+](=C6)C)C=C3
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| InChi Key |
PYJCATLYPXPYHF-UHFFFAOYSA-N
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| InChi Code |
InChI=1S/C34H24N6O2.2CHF3O3S/c1-39-19-25(17-23-7-3-5-9-29(23)39)35-33(41)27-15-13-21-11-12-22-14-16-28(38-32(22)31(21)37-27)34(42)36-26-18-24-8-4-6-10-30(24)40(2)20-262*2-1(3,4)8(5,6)7/h3-20H,1-2H32*(H,5,6,7)
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| Chemical Name |
2-N,9-N-bis(1-methylquinolin-1-ium-3-yl)-1,10-phenanthroline-2,9-dicarboxamide;trifluoromethanesulfonate
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| Synonyms |
PhenDC3 Phen-DC3 Phen DC3
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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 : ≥ 34 mg/mL (~40.06 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.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 1.4292 mL | 7.1461 mL | 14.2922 mL | |
| 5 mM | 0.2858 mL | 1.4292 mL | 2.8584 mL | |
| 10 mM | 0.1429 mL | 0.7146 mL | 1.4292 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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