Cat. No.: HY-15594

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Phen-DC3

Name: Phen-DC3
Brand: MedChemExpress
SKU: HY-15594
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12 Cited Publications

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Based on 12 publication(s) in Google Scholar

Phen-DC3 is a bisquinolinium G-quadruplex (G4) ligand. Phen-DC3 selectively binds to and stabilizes the hybrid quadruplex-duplex hybrid (QDH) derived from the PIM1 promoter. Phen-DC3 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 (HY-15594A) downregulates LPS (HY-D1056)-induced TNFRSF21, RIPK3 and p-MLKL in VECs, and ameliorates CLP-induced pulmonary vascular leakage in septic rats. Phen-DC3 can be used in studies related to neurodegenerative diseases and sepsis-associated vascular injury.

For research use only. We do not sell to patients.

CAS No.: 942936-75-6
Formula: C₃₄H₂₆N₆O₂
Molecular Weight:550.61

Storage:

Please store the product under the recommended conditions in the Certificate of Analysis.

Data Sheet (283 KB)

Phen-DC3 Chemical Structure

CAS No.: 942936-75-6

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Top Publications Citing

Use of MCE Products

Fluorescent Dye

Strong Fluorescence Signal / Multi-Disciplinary Applications / High Fluorescence Specificity

Biological Activity
- Description
- Cellular Effect
- In Vitro
- In Vivo
Chemical Information
Publications (12)
Solvent & Solubility
- In Vitro
Purity & Documentation
References
Help & FAQs
Classifications
Bioz

Biological Activity

Description

All α-synuclein Isoforms :

All RIP kinase Isoforms :

Cellular Effect

Cell Line	Type	Value	Description	References
HEK-293T	IC₅₀	1.5 nM Compound: phen-DC3	Inhibition of human telomerase expressed in HEK293T cells treated before telomerase elongation by telomeric repeat amplification protocol assay Inhibition of human telomerase expressed in HEK293T cells treated before telomerase elongation by telomeric repeat amplification protocol assay	[PMID: 17954919]
HEK-293T	IC₅₀	1500 nM Compound: phen-DC3	Inhibition of human telomerase expressed in HEK293T cells in presence of primer TS by primer extension assay Inhibition of human telomerase expressed in HEK293T cells in presence of primer TS by primer extension assay	[PMID: 17954919]
HEK-293T	IC₅₀	2.2 nM Compound: phen-DC3	Inhibition of human telomerase expressed in HEK293T cells treated after telomerase elongation by telomeric repeat amplification protocol assay Inhibition of human telomerase expressed in HEK293T cells treated after telomerase elongation by telomeric repeat amplification protocol assay	[PMID: 17954919]
HEK-293T	IC₅₀	63 nM Compound: phen-DC3	Inhibition of human telomerase expressed in in HEK293T cells in presence of primer (T2AG3)4 by primer extension assay Inhibition of human telomerase expressed in in HEK293T cells in presence of primer (T2AG3)4 by primer extension assay	[PMID: 17954919]
HEK-293T	IC₅₀	790 nM Compound: phen-DC3	Inhibition of human telomerase expressed in HEK293T cells in presence of primer (T2AG3)3 by primer extension assay Inhibition of human telomerase expressed in HEK293T cells in presence of primer (T2AG3)3 by primer extension assay	[PMID: 17954919]

In Vitro

Phen-DC3 (10 μM; 12 h) 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) 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) 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) 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-DC3 induces 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 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) 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) 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.

Cell Viability Assay^[4]

Cell Line:

Primary rat pulmonary VECs stimulated with LPS
Concentration:

Phen-DC3 trifluoromethanesulfonate: 10 μM; LPS: 10 μg/mL
Incubation Time:

12 h
Result:

mproved cell viability by 48.0%.

Western Blot Analysis^[4]

Cell Line:

Primary rat pulmonary VECs stimulated with LPS
Concentration:

Phen-DC3 trifluoromethanesulfonate: 10 μM; LPS: 10 μg/mL
Incubation Time:

12 h
Result:

Reduced TNFRSF21, RIPK3 and p-MLKL without significantly affecting RIPK1 or MLKL.

In Vivo

Phen-DC3 (1 mg/kg; i.v.; single dose; 12 hours post-CLP) improves sepsis-induced pulmonary vascular leakage in adult Sprague-Dawley rats^[4].
Phen-DC3 (~100-140 μM; microinjection) 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.

Animal Model:

Sprague-Dawley (adult, fasted 12 hours pre-surgery, sepsis induced by cecal ligation and puncture)^[4]
Dosage:

1 mg/kg
Administration:

i.v.; single dose; 12 hours post-CLP
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

CAS No. 942936-75-6
Molecular Weight 550.61
Formula C₃₄H₂₆N₆O₂
SMILES

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
Shipping

Room temperature in continental US; may vary elsewhere.
Storage

Please store the product under the recommended conditions in the Certificate of Analysis.

Publications (12)

All RT-PCRBio/Physico-chemical AssayCell Proliferation/Viability AssayFlow Cytometry

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Journal Impact Factor

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

G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity. [Abstract]

2024 Mar 21;52(5):2142-2156. PMID: 38340342
Cell Death Dis

MeCP2 duplication causes hyperandrogenism by upregulating LHCGR and downregulating RORα. [Abstract]

2021 Oct 25;12(11):999. PMID: 34697294

Phen-DC3 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.
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 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.
Int J Biol Macromol

I-motif formation in the promoter region of the B-MYB proto-oncogene. [Abstract]

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
iScience

2026 May 22;29(6):116036.
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 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 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 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).
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

Targeting DHODH promoter G-quadruplex to induce ferroptosis in melanoma cells. [Abstract]

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
Patent

US20210188889A1.

Solvent & Solubility

In Vitro:

DMSO : ≥ 34 mg/mL (61.75 mM; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)

* "≥" means soluble, but saturation unknown.

View the Complete Stock Solution Preparation Table

Preparing Stock Solutions

View the Complete Stock Solution Preparation Table

Concentration Solvent Mass

1 mg

5 mg

10 mg

Concentration

Solvent

Mass

1 mM

1.8162 mL

9.0808 mL

18.1617 mL

5 mM

0.3632 mL

1.8162 mL

3.6323 mL

10 mM

0.1816 mL

0.9081 mL

1.8162 mL

Molarity Calculator

Mass (g) = Concentration (mol/L) × Volume (L) × Molecular Weight (g/mol)

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Purity & Documentation

Select Batch:

Purity: 99.98%

Assay: 99.98%

ee.: 99.98%

Data Sheet (283 KB)
COA (2659 KB)
Elemental Analysis Report (2659 KB)
HNMR (2659 KB)
CNMR (2659 KB)
RP-HPLC (2659 KB)
NP-HPLC (2659 KB)
MS (2659 KB)
LCMS (2659 KB)
IR (2659 KB)
GC (2659 KB)
OR (2659 KB)
SDS-PAGE (2659 KB)
SEC-HPLC (2659 KB)
Other Report (2659 KB)
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]

Help & FAQs

How should lyophilized recombinant proteins be reconstituted and stored?

1. Before opening the cap, centrifuge the vial at 13000 rpm for 20-30 seconds. This step will ensure that any lyophilized powder that may have adhered to the cap or walls is collected at the bottom of the vial, minimizing the risk of product loss.

Complete Stock Solution Preparation Table

Optional Solvent	Concentration Solvent Mass	1 mg	5 mg	10 mg	25 mg
DMSO	1 mM	1.8162 mL	9.0808 mL	18.1617 mL	45.4042 mL
	5 mM	0.3632 mL	1.8162 mL	3.6323 mL	9.0808 mL
	10 mM	0.1816 mL	0.9081 mL	1.8162 mL	4.5404 mL
	15 mM	0.1211 mL	0.6054 mL	1.2108 mL	3.0269 mL
	20 mM	0.0908 mL	0.4540 mL	0.9081 mL	2.2702 mL
	25 mM	0.0726 mL	0.3632 mL	0.7265 mL	1.8162 mL
	30 mM	0.0605 mL	0.3027 mL	0.6054 mL	1.5135 mL
	40 mM	0.0454 mL	0.2270 mL	0.4540 mL	1.1351 mL
	50 mM	0.0363 mL	0.1816 mL	0.3632 mL	0.9081 mL
	60 mM	0.0303 mL	0.1513 mL	0.3027 mL	0.7567 mL

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Phen-DC3

Publications Citing Use of MedChemExpress (MCE) Phen-DC3

All α-synuclein Isoforms

All RIP kinase Isoforms

Biological Activity

Chemical Information

Publications (12)

Solvent & Solubility

Purity & Documentation

References

Help & FAQs

Complete Stock Solution Preparation Table

Phen-DC3 Related Classifications

HY-15594 Related Classifications

Bioz