Phen-DC3 Trifluoromethanesulfonate
Based on 12 publication(s) in Google Scholar
Phen-DC3 Trifluoromethanesulfonate is a bisquinolinium G-quadruplex (G4) ligand. Phen-DC3 Trifluoromethanesulfonate selectively binds to and stabilizes the hybrid quadruplex-duplex hybrid (QDH) derived from the PIM1 promoter. Phen-DC3 Trifluoromethanesulfonate also binds to the c-myc promoter Pu24T G4 via extensive π-stacking, and induces polymerase stalling at α-synuclein DNA and RNA G4 sequences. Phen-DC3 Trifluoromethanesulfonate downregulates LPS (HY-D1056)-induced TNFRSF21, RIPK3 and p-MLKL in VECs, and ameliorates CLP-induced pulmonary vascular leakage in septic rats. Phen-DC3 Trifluoromethanesulfonate can be used in studies related to neurodegenerative diseases and sepsis-associated vascular injury.
For research use only. We do not sell to patients.
- Purity: 98.64%
- CAS No.: 929895-45-4
- Formula: C36H26F6N6O8S2
- Molecular Weight:848.75
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Storage:
4°C, sealed storage, away from moisture
* In solvent : -80°C, 6 months; -20°C, 1 month (sealed storage, away from moisture)
To place orders, for customer services and technical support, please contact: MedChemExpress USA
Tel: 609-228-6898 E-mail: [email protected] [email protected]
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Biological Activity
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Chemical Information
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Solvent & Solubility
- Purity & Documentation
- References
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Publications Citing Use of MedChemExpress (MCE) Phen-DC3 Trifluoromethanesulfonate
More- Nucleic Acids Res. 2026 Jan 14;54(2):gkaf1481. [Abstract]
- Nucleic Acids Res. 2024 Mar 21;52(5):2142-2156. [Abstract]
- Cell Death Dis. 2021 Oct 25;12(11):999. [Abstract]
- Int J Biol Macromol. 2025 Jun 20;319(Pt 1):145405. [Abstract]
- Int J Biol Macromol. 2025 Mar:296:139582. [Abstract]
- J Mol Med (Berl). 2026 Apr 23;104(1):68. [Abstract]
- iScience. 2026 May 22;29(6):116036.
- iScience. 2022 Oct 9;25(11):105312. [Abstract]
- J Phys Chem B. 2023 Jul 6;127(26):5859-5868. [Abstract]
- Biochem Biophys Res Commun. 2026 Jan 8:795:153117. [Abstract]
- Res Vet Sci. 2026 Jul:206:106188. [Abstract]
- Patent. US20210188889A1.
Customer Validation & Images
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Bio/Physico-chemical Assay
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Cell Proliferation/Viability Assay
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RT-PCR
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Flow Cytometry
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RT-PCR
All α-synuclein Isoforms
More
Biological Activity
Phen-DC3(10 μM; 12 h) Trifluoromethanesulfonate reduces the expression of TNFRSF21, enhances cell viability, decreases cell permeability, and inhibits the expression of necroptosis markers (p-MLKL, RIPK3) in lipopolysaccharide (LPS)-stimulated primary rat pulmonary vein vascular endothelial cells (VECs)[4].
Phen-DC3 (20-60 μM; 24 h) Trifluoromethanesulfonate selectively stabilizes the hybrid QDH conformations of SO7 and SO8 derived from the PIM1 oncogene, increasing their melting temperatures by 13.5°C and 14.2°C, respectively, at a 1:1 ratio, while exerting minimal stabilizing effects on the antiparallel QDH SO2[1].
Phen-DC3(0.1-0.5 mM; 24 h) Trifluoromethanesulfonate binds rigidly and specifically to the Q-D linker region of the chimeric PIM1 QDH SO7 in a single well-defined conformation, a characteristic determined by high-resolution NMR spectroscopy[1].
Phen-DC3(1.5 mM) Trifluoromethanesulfonate selectively binds to and stabilizes the heterozygous conformation of polymorphic PIM1 QDH SO8-F in vitro, shifting its conformational equilibrium from a 50:50 heterozygous/antiparallel mixture to a single heterozygous complex[1].
Phen-DC3Trifluoromethanesulfonate nduces differential changes in nucleotide accessibility in wild-type (WT) and single-nucleotide polymorphism (SNP) α-synuclein RNA sequences, with the strongest effect (6- to 8-fold change) observed in SNP-511 RNA[2].
Phen-DC3 Trifluoromethanesulfonate regulates the accessibility of guanine in the DNA sequences of wild-type (WT) and single nucleotide polymorphism (SNP) α-synuclein, reducing the accessibility of SNP-877, SNP-962 and SNP-875 DNA by approximately 2-fold, which indicates its G4-stabilizing activity[2].
Phen-DC3 (9 equiv; under conditions supporting Taq polymerase activity at 37 °C) Trifluoromethanesulfonate potently induces Taq polymerase stalling in all wild-type (WT) and single nucleotide polymorphism (SNP) α-synuclein DNA sequences, with the highest stalling activity observed in WT DNA (a 47.7-fold change relative to KCl) and a comparable activity in SNP-875 DNA (a 47.1-fold change)[2].
Phen-DC3 (DNA/ligand ratio 1:0.5-1:2; NOESY mixing times 200-700 ms; 25 °C) Trifluoromethanesulfonate forms a 1:1 complex with the Pu24T G-quadruplex in the human c-myc promoter via extensive π-stacking interactions with the 5'-terminal top G-quadruplex. This interaction increases the thermal stability of the G-quadruplex by approximately 12 °C and exhibits submicromolar to nanomolar binding affinity[3].
MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.
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Cell Line:Primary rat pulmonary VECs stimulated with LPS
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Concentration:Phen-DC3 trifluoromethanesulfonate: 10 μM; LPS: 10 μg/mL
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Incubation Time:12 h
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Result:mproved cell viability by 48.0%.
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Cell Line:Primary rat pulmonary VECs stimulated with LPS
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Concentration:Phen-DC3 trifluoromethanesulfonate: 10 μM; LPS: 10 μg/mL
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Incubation Time:12 h
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Result:Reduced TNFRSF21, RIPK3 and p-MLKL without significantly affecting RIPK1 or MLKL.
Phen-DC3 (~100-140 μM; microinjection) Trifluoromethanesulfonate selectively binds and stabilizes the hybrid conformation of PIM1 QDH within the intracellular environment of Xenopus laevis oocytes, overriding the native cellular preference for the antiparallel QDH form[1].
MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.
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Animal Model:Sprague-Dawley (adult, fasted 12 hours pre-surgery, sepsis induced by cecal ligation and puncture)[4]
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Dosage:1 mg/kg
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Administration:i.v.; single dose; 12 hours post-CLP
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Result:Reduced pulmonary vascular permeability to Evans Blue, as shown by a significant decrease in the ratio of Evans Blue mass to protein mass in lung tissue compared to untreated septic rats.
Chemical Information
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CAS No. 929895-45-4
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Appearance Solid
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Molecular Weight 848.75
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Formula C36H26F6N6O8S2
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Color White to light yellow
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SMILES
[O-]S(=O)(C(F)(F)F)=O.C[N+]1=C2C=CC=CC2=CC(NC(C3=CC=C4C=CC5=CC=C(C(NC6=C[N+](C)=C7C=CC=CC7=C6)=O)N=C5C4=N3)=O)=C1.[O-]S(=O)(C(F)(F)F)=O
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Synonyms
Phen-DC3 Triflate
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Shipping
Room temperature in continental US; may vary elsewhere.
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Storage
4°C, sealed storage, away from moisture
* In solvent : -80°C, 6 months; -20°C, 1 month (sealed storage, away from moisture)
Publications (12)
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Journal Impact Factor
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Most Recent
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Nucleic Acids Res
RNA G-quadruplexes promote codon repeat-associated ribosomal frameshifting in human genes. [Abstract]2026 Jan 14;54(2):gkaf1481. PMID: 41543171 -
Nucleic Acids Res
2024 Mar 21;52(5):2142-2156. PMID: 38340342 -
Cell Death Dis
2021 Oct 25;12(11):999. PMID: 34697294
Phen-DC3 Trifluoromethanesulfonate purchased from MedChemExpress. Usage Cited in: Cell Death Dis. 2021 Oct 25;12(11):999. [Abstract]
The relative enrichment of G-quadruplexes (G4) in Lhcgr CGI-II from TM3 cells treated with vehicle or 10 μM 5-ALA, 5 μM 360 A iodide, or 10 μM Phen-DC3 Trifluoromethanesulfonate (Phen-DC3) (48 h) by ChIP-qPCR analysis. The G-quadruplex antibody (BG4) or IgG were used, respectively. N = 3 for each group.
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Int J Biol Macromol
An RNA G-quadruplex within the sclerostin 3' untranslated region enhances sclerostin expression by blocking miR-4648 binding. [Abstract]2025 Jun 20;319(Pt 1):145405. PMID: 40545075
Phen-DC3 Trifluoromethanesulfonate purchased from MedChemExpress. Usage Cited in: Int J Biol Macromol. 2025 Jun 20;319(Pt 1):145405. [Abstract]
FRET-MC profiles were obtained under different experimental conditions: (1) 0.2 μM F21T alone (black line), (2) 0.2 μM F21T with 0.4 μM Phen-DC3 Trifluoromethanesulfonate (PhenDC3) (red line), (3) 0.2 μM F21T with 0.4 μM PhenDC3 and 2 μM SOST RG4wt competitors (blue line), and (4) 0.2 μM F21T with 0.4 μM PhenDC3 and 2 μM SOST RG4mut competitors (purple line). The FRET-MC buffer was composed of 10 mM KCl, 90 mM LiCl, and 10 mM lithium cacodylate at pH 7.2.
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Int J Biol Macromol
2025 Mar:296:139582. PMID: 39798757 -
J Mol Med (Berl)
The role and mechanism of TNFRSF21 in promoting necroptosis of vascular endothelial cells and inducing vascular leakage in sepsis. [Abstract]2026 Apr 23;104(1):68. PMID: 42020785 -
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iScience
Genomic G-quadruplex folding triggers a cytokine-mediated inflammatory feedback loop to aggravate inflammatory diseases. [Abstract]2022 Oct 9;25(11):105312. PMID: 36304116
Phen-DC3 Trifluoromethanesulfonate purchased from MedChemExpress. Usage Cited in: iScience. 2022 Oct 9;25(11):105312. [Abstract]
Cell viability was analyzed using a CCK-8 kit under the G4 stabilizer treatment for 12 h, 24 h, and 48 h. Phen-DC3 Trifluoromethanesulfonate (Phen-DC3) (5-100 nM)-induced G4 stabilization inhibited NP cell viability in a dose-dependent manner.
Phen-DC3 Trifluoromethanesulfonate purchased from MedChemExpress. Usage Cited in: iScience. 2022 Oct 9;25(11):105312. [Abstract]
mRNA expression of Il6 after the single or combined treatment of PDS, Braco-19, Phen-DC3 Trifluoromethanesulfonate (Phen-DC3) (5-20 nM) and IL-1β (10 ng/mL). Phen-DC3 promoted Il6 mRNA expression in NP cells in a dose-dependent manner by stabilizing genomic G4 structures.
Phen-DC3 Trifluoromethanesulfonate purchased from MedChemExpress. Usage Cited in: iScience. 2022 Oct 9;25(11):105312. [Abstract]
Flow cytometry assay for the cell apoptosis under the treatment of PDS, Braco-19, and Phen-DC3 Trifluoromethanesulfonate (Phen-DC3) (5-20 nM).
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J Phys Chem B
Nonselective Intercalation of G-Quadruplex-Targeting Ligands into Double-Stranded DNA Quantified by Single-Molecule Stretching. [Abstract]2023 Jul 6;127(26):5859-5868. PMID: 37357414 -
Biochem Biophys Res Commun
2026 Jan 8:795:153117. PMID: 41380445 -
Res Vet Sci
HnRNP H1 binds to nucleocapsid protein and potential guanine-quadruplex site of viral RNA to promote PRRSV-2 proliferation. [Abstract]2026 Jul:206:106188. PMID: 41996971 -
Solvent & Solubility
DMSO : ≥ 34 mg/mL (40.06 mM; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)
* "≥" means soluble, but saturation unknown.
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month (sealed storage, away from moisture). When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month (sealed storage, away from moisture). When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
Concentration (start) × Volume (start) = Concentration (final) × Volume (final)
Purity & Documentation
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Data Sheet (288 KB)
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SDS (252 KB)
- English - EN (252 KB)
- Français - FR (252 KB)
- Deutsch - DE (252 KB)
- Norwegian - NO (252 KB)
- Español - ES (252 KB)
- Swedish - SV (252 KB)
- Italian - IT (252 KB)
- Korean - KR (252 KB)
- Portuguese - PT (252 KB)
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Handling Instructions (2659 KB)
References
[1]. Ghosh A, et al. Structural basis of bis-quinolinium ligands binding to quadruplex-duplex hybrids from PIM1 oncogene. Nucleic acids research. 2025 Sep 05;53(17):gkaf894. [Content Brief]
[2]. Turcotte MA, et al. Pathogenic SNPs Affect Both RNA and DNA G-Quadruplexes' Responses to Ligands. ACS chemical biology. 2024 May 17;19(5):1045-1050. [Content Brief]
[3]. Chung WJ, et al. Solution structure of a G-quadruplex bound to the bisquinolinium compound Phen-DC(3). Angewandte Chemie (International ed. in English). 2014 Jan 20;53(4):999-1002. [Content Brief]
[4]. Wang J, et al. The role and mechanism of TNFRSF21 in promoting necroptosis of vascular endothelial cells and inducing vascular leakage in sepsis. Journal of molecular medicine (Berlin, Germany). 2026 Apr 23;104(1):68. [Content Brief]
Complete Stock Solution Preparation Table
Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.
Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month (sealed storage, away from moisture). When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.
| Optional Solvent | Concentration Solvent Mass | 1 mg | 5 mg | 10 mg | 25 mg |
|---|---|---|---|---|---|
| DMSO | 1 mM | 1.1782 mL | 5.8910 mL | 11.7820 mL | 29.4551 mL |
| 5 mM | 0.2356 mL | 1.1782 mL | 2.3564 mL | 5.8910 mL | |
| 10 mM | 0.1178 mL | 0.5891 mL | 1.1782 mL | 2.9455 mL | |
| 15 mM | 0.0785 mL | 0.3927 mL | 0.7855 mL | 1.9637 mL | |
| 20 mM | 0.0589 mL | 0.2946 mL | 0.5891 mL | 1.4728 mL | |
| 25 mM | 0.0471 mL | 0.2356 mL | 0.4713 mL | 1.1782 mL | |
| 30 mM | 0.0393 mL | 0.1964 mL | 0.3927 mL | 0.9818 mL | |
| 40 mM | 0.0295 mL | 0.1473 mL | 0.2946 mL | 0.7364 mL |
Phen-DC3 Trifluoromethanesulfonate Related Classifications
HY-15594A Related Classifications
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