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MedKoo Cat#: 561777 | Name: PhenDC3
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Description:

WARNING: This product is for research use only, not for human or veterinary use.

PhenDC3 is a highly selective telomeric G-quadruplex-DNA binding probe.

Chemical Structure

PhenDC3
PhenDC3
CAS#929895-45-4 (triflate)

Theoretical Analysis

MedKoo Cat#: 561777

Name: PhenDC3

CAS#: 929895-45-4 (triflate)

Chemical Formula: C36H26F6N6O8S2

Exact Mass: 848.1158

Molecular Weight: 848.75

Elemental Analysis: C, 50.95; H, 3.09; F, 13.43; N, 9.90; O, 15.08; S, 7.55

Price and Availability

Size Price Availability Quantity
5mg USD 450.00 2 Weeks
25mg USD 950.00 2 Weeks
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Related CAS #
942936-75-6 (free base) 929895-45-4 (triflate) 2225806-29-9 (iodide) 1644168-15-9 (mesylate)
Synonym
PhenDC3; Phen-DC3; Phen DC3; Phen-DC(3);
IUPAC/Chemical Name
3,3'-((1,10-Phenanthroline-2,9-dicarbonyl)bis(azanediyl))bis(1-methylquinolin-1-ium) bis-triflate
InChi Key
PYJCATLYPXPYHF-UHFFFAOYSA-N
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)20-26;2*2-1(3,4)8(5,6)7/h3-20H,1-2H3;2*(H,5,6,7)
SMILES Code
O=C(NC1=C[N+](C)=C2C=CC=CC2=C1)C3=NC4=C5N=C(C(NC6=C[N+](C)=C7C=CC=CC7=C6)=O)C=CC5=CC=C4C=C3.O=S([O-])(C(F)(F)F)=O.O=S([O-])(C(F)(F)F)=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
Soluble in DMSO
Shelf Life
>2 years if stored properly
Drug Formulation
This drug may be formulated in DMSO
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
More Info
Product Data
Product Data
Instruction
View handling instruction
Biological target:
Phen-DC3 Trifluoromethanesulfonate is a G-quadruplex (G4) specific ligand which can inhibit FANCJ and DinG helicases with IC50s of 65±6 and 50±10 nM, respectively.
In vitro activity:
This study reports that Phen-DC3, one of the most prominent G-quadruplex ligands in terms of high binding affinity and selectivity, causes dTAGGG(TTAGGG)3 to completely change its fold in KCl solution from a hybrid-1 to an antiparallel chair-type structure, wherein the ligand intercalates between a two-quartet unit and a pseudo-quartet, thereby ejecting one potassium ion. This unprecedented high-resolution NMR structure shows for the first time a true ligand intercalation into an intramolecular G-quadruplex. Reference: Angew Chem Int Ed Engl. 2022 Oct 4;61(40):e202207384. https://pubmed.ncbi.nlm.nih.gov/35993443/
In vivo activity:
TBD
Solvent mg/mL mM comments
Solubility
DMSO 67.0 78.94
Note: There can be variations in solubility for the same chemical from different vendors or different batches from the same vendor. The following factors can affect the solubility of the same chemical: solvent used for crystallization, residual solvent content, polymorphism, salt versus free form, degree of hydration, solvent temperature. Please use the solubility data as a reference only. Warming and sonication will facilitate dissolving. Still have questions? Please contact our Technical Support scientists.

Preparing Stock Solutions

The following data is based on the product molecular weight 848.75 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.

Recalculate based on batch purity %
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. Ghosh A, Trajkovski M, Teulade-Fichou MP, Gabelica V, Plavec J. Phen-DC3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation. Angew Chem Int Ed Engl. 2022 Oct 4;61(40):e202207384. doi: 10.1002/anie.202207384. Epub 2022 Sep 2. PMID: 35993443; PMCID: PMC9826182. 2. Matsumoto K, Okamoto K, Okabe S, Fujii R, Ueda K, Ohashi K, Seimiya H. G-quadruplex-forming nucleic acids interact with splicing factor 3B subunit 2 and suppress innate immune gene expression. Genes Cells. 2021 Feb;26(2):65-82. doi: 10.1111/gtc.12824. Epub 2021 Jan 5. PMID: 33290632; PMCID: PMC7898707.
In vitro protocol:
1. Ghosh A, Trajkovski M, Teulade-Fichou MP, Gabelica V, Plavec J. Phen-DC3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation. Angew Chem Int Ed Engl. 2022 Oct 4;61(40):e202207384. doi: 10.1002/anie.202207384. Epub 2022 Sep 2. PMID: 35993443; PMCID: PMC9826182. 2. Matsumoto K, Okamoto K, Okabe S, Fujii R, Ueda K, Ohashi K, Seimiya H. G-quadruplex-forming nucleic acids interact with splicing factor 3B subunit 2 and suppress innate immune gene expression. Genes Cells. 2021 Feb;26(2):65-82. doi: 10.1111/gtc.12824. Epub 2021 Jan 5. PMID: 33290632; PMCID: PMC7898707.
In vivo protocol:
TBD
1: Hegedus L, Toth A, Harami GM, Palinkas J, Karatayeva N, Sajben-Nagy E, Bene S, Afzali Jaktajdinani S, Kovacs M, Juhasz S, Burkovics P. Werner helicase interacting protein 1 contributes to G-quadruplex processing in human cells. Sci Rep. 2024 Jul 8;14(1):15740. doi: 10.1038/s41598-024-66425-y. PMID: 38977862; PMCID: PMC11231340. 2: Turcotte MA, Perreault JP. Pathogenic SNPs Affect Both RNA and DNA G-Quadruplexes' Responses to Ligands. ACS Chem Biol. 2024 May 17;19(5):1045-1050. doi: 10.1021/acschembio.4c00104. Epub 2024 Apr 30. PMID: 38688038; PMCID: PMC11106744. 3: Laigre E, Bonnet H, Beauvineau C, Lavergne T, Verga D, Defrancq E, Dejeu J, Teulade-Fichou MP. Systematic Evaluation of Benchmark G4 Probes and G4 Clinical Drugs using three Biophysical Methods: A Guideline to Evaluate Rapidly G4-Binding Affinity. Chembiochem. 2024 Jun 17;25(12):e202400210. doi: 10.1002/cbic.202400210. Epub 2024 May 17. PMID: 38619969. 4: Vianney YM, Dierks D, Weisz K. Structural Differences at Quadruplex-Duplex Interfaces Enable Ligand-Induced Topological Transitions. Adv Sci (Weinh). 2024 Jun;11(24):e2309891. doi: 10.1002/advs.202309891. Epub 2024 Mar 13. PMID: 38477454; PMCID: PMC11200018. 5: Cervenak M, Molnár OR, Horváth P, Smeller L. Stabilization of G-Quadruplex Structures of the SARS-CoV-2 Genome by TMPyP4, BRACO19, and PhenDC3. Int J Mol Sci. 2024 Feb 20;25(5):2482. doi: 10.3390/ijms25052482. PMID: 38473730; PMCID: PMC10931149. 6: Nicolás Á, Quero JG, Barroso M, Gándara Z, Gude L. DNA Interactions and Biological Activity of 2,9-Disubstituted 1,10-Phenanthroline Thiosemicarbazone- Based Ligands and a 4-Phenylthiazole Derivative. Biology (Basel). 2024 Jan 20;13(1):60. doi: 10.3390/biology13010060. PMID: 38275736; PMCID: PMC10813753. 7: Zareie AR, Dabral P, Verma SC. G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection. Pathogens. 2024 Jan 8;13(1):60. doi: 10.3390/pathogens13010060. PMID: 38251367; PMCID: PMC10819198. 8: Le Sénéchal R, Keruzoré M, Quillévéré A, Loaëc N, Dinh VT, Reznichenko O, Guixens-Gallardo P, Corcos L, Teulade-Fichou MP, Granzhan A, Blondel M. Alternative splicing of BCL-x is controlled by RBM25 binding to a G-quadruplex in BCL-x pre-mRNA. Nucleic Acids Res. 2023 Nov 10;51(20):11239-11257. doi: 10.1093/nar/gkad772. PMID: 37811881; PMCID: PMC10639069. 9: Lejault P, Prudent L, Terrier MP, Perreault JP. Small molecule chaperones facilitate the folding of RNA G-quadruplexes. Biochimie. 2023 Nov;214(Pt A):83-90. doi: 10.1016/j.biochi.2023.08.016. Epub 2023 Sep 4. PMID: 37666291. 10: De Piante E, D'Aria F, Napolitano LMR, Amato J, Pirrello S, Onesti S, Giancola C. Exploring the G-quadruplex binding and unwinding activity of the bacterial FeS helicase DinG. Sci Rep. 2023 Aug 3;13(1):12610. doi: 10.1038/s41598-023-39675-5. PMID: 37537265; PMCID: PMC10400533. 11: Liu T, Wu Y, Qin L, Luo Q, Li W, Cheng Y, Tu Y, You H. Nonselective Intercalation of G-Quadruplex-Targeting Ligands into Double-Stranded DNA Quantified by Single-Molecule Stretching. J Phys Chem B. 2023 Jul 6;127(26):5859-5868. doi: 10.1021/acs.jpcb.3c03031. Epub 2023 Jun 25. PMID: 37357414. 12: Real-Hohn A, Groznica M, Kontaxis G, Zhu R, Chaves OA, Vazquez L, Hinterdorfer P, Kowalski H, Blaas D. Stabilization of the Quadruplex-Forming G-Rich Sequences in the Rhinovirus Genome Inhibits Uncoating-Role of Na+ and K. Viruses. 2023 Apr 19;15(4):1003. doi: 10.3390/v15041003. PMID: 37112983; PMCID: PMC10141139. 13: Chashchina GV, Tevonyan LL, Beniaminov AD, Kaluzhny DN. Taq-Polymerase Stop Assay to Determine Target Selectivity of G4 Ligands in Native Promoter Sequences of MYC, TERT, and KIT Oncogenes. Pharmaceuticals (Basel). 2023 Apr 5;16(4):544. doi: 10.3390/ph16040544. PMID: 37111301; PMCID: PMC10142109. 14: Szeltner Z, Ferenc G, Juhász T, Kupihár Z, Váradi Z, Szüts D, Kovács L. Probing telomeric-like G4 structures with full or partial 2'-deoxy-5-hydroxyuridine substitutions. Biochimie. 2023 Nov;214(Pt A):33-44. doi: 10.1016/j.biochi.2023.01.009. Epub 2023 Jan 24. PMID: 36707016. 15: Holden L, Gkika KS, Burke CS, Long C, Keyes TE. Selective, Disruptive Luminescent Ru(II) Polypyridyl Probes of G-Quadruplex. Inorg Chem. 2023 Feb 6;62(5):2213-2227. doi: 10.1021/acs.inorgchem.2c03903. Epub 2023 Jan 26. PMID: 36703307; PMCID: PMC9906756. 16: Yu Z, Spiegel J, Melidis L, Hui WWI, Zhang X, Radzevičius A, Balasubramanian S. Chem-map profiles drug binding to chromatin in cells. Nat Biotechnol. 2023 Sep;41(9):1265-1271. doi: 10.1038/s41587-022-01636-0. Epub 2023 Jan 23. PMID: 36690761; PMCID: PMC10497411. 17: Moreira D, Leitão D, Lopes-Nunes J, Santos T, Figueiredo J, Miranda A, Alexandre D, Tomaz C, Mergny JL, Cruz C. G-Quadruplex Aptamer-Ligand Characterization. Molecules. 2022 Oct 11;27(20):6781. doi: 10.3390/molecules27206781. PMID: 36296374; PMCID: PMC9609330. 18: Das P, Phan AT. Tetrad-binding ligands do not bind specifically to left- handed G-quadruplexes. Chem Commun (Camb). 2022 Oct 6;58(80):11264-11267. doi: 10.1039/d2cc03374g. PMID: 36112098. 19: Ghosh A, Trajkovski M, Teulade-Fichou MP, Gabelica V, Plavec J. Phen- DC3 Induces Refolding of Human Telomeric DNA into a Chair-Type Antiparallel G-Quadruplex through Ligand Intercalation. Angew Chem Int Ed Engl. 2022 Oct 4;61(40):e202207384. doi: 10.1002/anie.202207384. Epub 2022 Sep 2. PMID: 35993443; PMCID: PMC9826182. 20: Luo Y, Verga D, Mergny JL. Iso-FRET: an isothermal competition assay to analyze quadruplex formation in vitro. Nucleic Acids Res. 2022 Sep 9;50(16):e93. doi: 10.1093/nar/gkac465. PMID: 35670668; PMCID: PMC9458428.