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PhenDC3

Alias: PhenDC3 Phen-DC3 Phen DC3
Cat No.:V6873 Purity: ≥98%
Phen-DC3 Trifluoromethanesulfonate is a G4-specific ligand that can inhibit helicases FANCJ and DinG with IC50s values of 65±6 and 50±10 nM respectively.
PhenDC3
PhenDC3 Chemical Structure CAS No.: 929895-45-4
Product category: New1
This product is for research use only, not for human use. We do not sell to patients.
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1mg
5mg
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Other Forms of PhenDC3:

  • Phen-DC3
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Purity & Quality Control Documentation

Purity: ≥98%

Product Description
Phen-DC3 Trifluoromethanesulfonate is a G4-specific ligand that can inhibit helicases FANCJ and DinG with IC50s values of 65±6 and 50±10 nM respectively.
Biological Activity I Assay Protocols (From Reference)
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].
References

[1]. Specialization among Iron-Sulfur Cluster Helicases to Resolve G-quadruplex DNA Structures That Threaten Genomic Stability. J Biol Chem. 2013 Sep 27; 288(39): 28217–28229.

[2]. Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites. EMBO J. 2015 Jun 12; 34(12): 1718–1734.

These protocols are for reference only. InvivoChem does not independently validate these methods.
Physicochemical Properties
Molecular Formula
C35H26F3N6O5S
Molecular Weight
699.678356647491
Exact Mass
848.115
CAS #
929895-45-4
Related CAS #
Phen-DC3;942936-75-6
PubChem CID
131704505
Appearance
White to light yellow solid powder
Hydrogen Bond Donor Count
2
Hydrogen Bond Acceptor Count
16
Rotatable Bond Count
4
Heavy Atom Count
58
Complexity
1050
Defined Atom Stereocenter Count
0
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)20-262*2-1(3,4)8(5,6)7/h3-20H,1-2H32*(H,5,6,7)
Chemical Name
2-N,9-N-bis(1-methylquinolin-1-ium-3-yl)-1,10-phenanthroline-2,9-dicarboxamide;trifluoromethanesulfonate
Synonyms
PhenDC3 Phen-DC3 Phen DC3
HS Tariff Code
2934.99.9001
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)
Solubility Data
Solubility (In Vitro)
DMSO : ≥ 34 mg/mL (~40.06 mM)
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
(e.g. IP/IV/IM/SC)
Injection Formulation 1: DMSO : Tween 80: Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution 50 μL Tween 80 850 μL Saline)
*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 : PEG300Tween 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).
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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)]
*Preparation of 20% SBE-β-CD in Saline (4°C,1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution.
Injection Formulation 5: 2-Hydroxypropyl-β-cyclodextrin : Saline = 50 : 50 (i.e. 500 μL 2-Hydroxypropyl-β-cyclodextrin 500 μL Saline)
Injection Formulation 6: DMSO : PEG300 : castor oil : Saline = 5 : 10 : 20 : 65 (i.e. 50 μL DMSO 100 μLPEG300 200 μL castor oil 650 μL Saline)
Injection Formulation 7: Ethanol : Cremophor : Saline = 10: 10 : 80 (i.e. 100 μL Ethanol 100 μL Cremophor 800 μL Saline)
Injection Formulation 8: Dissolve in Cremophor/Ethanol (50 : 50), then diluted by Saline
Injection Formulation 9: EtOH : Corn oil = 10 : 90 (i.e. 100 μL EtOH 900 μL Corn oil)
Injection Formulation 10: EtOH : PEG300Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL EtOH 400 μLPEG300 50 μL Tween 80 450 μL 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).
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Oral Formulation 3: Dissolved in PEG400
Oral Formulation 4: Suspend in 0.2% Carboxymethyl cellulose
Oral Formulation 5: Dissolve in 0.25% Tween 80 and 0.5% Carboxymethyl cellulose
Oral Formulation 6: Mixing with food powders


Note: Please be aware that the above formulations are for reference only. InvivoChem strongly recommends customers to read literature methods/protocols carefully before determining which formulation you should use for in vivo studies, as different compounds have different solubility properties and have to be formulated differently.

 (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.

Calculator

Molarity Calculator allows you to calculate the mass, volume, and/or concentration required for a solution, as detailed below:

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An example of molarity calculation using the molarity calculator is shown below:
What is the mass of compound required to make a 10 mM stock solution in 5 ml of DMSO given that the molecular weight of the compound is 350.26 g/mol?
  • Enter 350.26 in the Molecular Weight (MW) box
  • Enter 10 in the Concentration box and choose the correct unit (mM)
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  • The answer of 17.513 mg appears in the Mass box. In a similar way, you may calculate the volume and concentration.

Dilution Calculator allows you to calculate how to dilute a stock solution of known concentrations. For example, you may Enter C1, C2 & V2 to calculate V1, as detailed below:

What volume of a given 10 mM stock solution is required to make 25 ml of a 25 μM solution?
Using the equation C1V1 = C2V2, where C1=10 mM, C2=25 μM, V2=25 ml and V1 is the unknown:
  • Enter 10 into the Concentration (Start) box and choose the correct unit (mM)
  • Enter 25 into the Concentration (End) box and select the correct unit (mM)
  • Enter 25 into the Volume (End) box and choose the correct unit (mL)
  • Click the “Calculate” button
  • The answer of 62.5 μL (0.1 ml) appears in the Volume (Start) box
g/mol

Molecular Weight Calculator allows you to calculate the molar mass and elemental composition of a compound, as detailed below:

Note: Chemical formula is case sensitive: C12H18N3O4  c12h18n3o4
Instructions to calculate molar mass (molecular weight) of a chemical compound:
  • To calculate molar mass of a chemical compound, please enter the chemical/molecular formula and click the “Calculate’ button.
Definitions of molecular mass, molecular weight, molar mass and molar weight:
  • Molecular mass (or molecular weight) is the mass of one molecule of a substance and is expressed in the unified atomic mass units (u). (1 u is equal to 1/12 the mass of one atom of carbon-12)
  • Molar mass (molar weight) is the mass of one mole of a substance and is expressed in g/mol.
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Reconstitution Calculator allows you to calculate the volume of solvent required to reconstitute your vial.

  • Enter the mass of the reagent and the desired reconstitution concentration as well as the correct units
  • Click the “Calculate” button
  • The answer appears in the Volume (to add to vial) box
In vivo Formulation Calculator (Clear solution)
Step 1: Enter information below (Recommended: An additional animal to make allowance for loss during the experiment)
Step 2: Enter in vivo formulation (This is only a calculator, not the exact formulation for a specific product. Please contact us first if there is no in vivo formulation in the solubility section.)
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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.

Biological Data
  • Heterogeneous instability phenotype of different G4-forming tandem repeats in WT cells treated or not with Phen-DC3, and inpif1Δ cells Motif sequence of different G4-forming tandem repeats. G4 motif is underlined. G-tracts are shown in bold. Thec-Myc,c-Kit, andBcl2-MBR G4-forming sequences have been separated by the neutral CEB1 spacer (in gray) to prevent the formation of irrelevant G4 conformations resulting from the tandem organization. Details about the minisatellite size, number of motifs, and GC content are provided in Supplementary Table S1.[2]. Aurèle Piazza, et al. Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites. EMBO J. 2015 Jun 12; 34(12): 1718–1734
  • A single 9-nt-long loop within the G4 motif is required and sufficient to stabilize the underlying minisatellite sequencein vivo Replacement of the central 9-nt loop ofCEB25-WT by a single T inCEB25-L111(T) results in the destabilization of the minisatellite in Phen-DC3-treated WT cells (ANT1903), and inpif1Δ cells (ANT1917). Replacement of a 1-nt loop ofCEB1-WT by the 9-nt-long central loop ofCEB25-WT inCEB1-loopCEB25 results in the stabilization of the minisatellite in Phen-DC3-treated WT cells (ORT7171), and inpif1Δ cells (ORT7186-5). The parentalCEB1-loopCEB25 allele (*) is 2 motifs shorter in thepif1Δ mutant than in WT cells (24 motifs instead of 26). All other alleles contain 26 motifs. Analysis was done as in Fig​Fig11B.[2]. Aurèle Piazza, et al. Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites. EMBO J. 2015 Jun 12; 34(12): 1718–1734
  • Southern blot analysis of CEB25 allele variants with shortened central loop length in WT cells treated with Phen-DC3 (top panel) andpif1Δ cells (bottom panel). From left to right: WT strains are ANT1903, ANT1904, ORT7333, ORT7334, and ANT1901;pif1Δ strains are ANT1917, ANT1918, ORT7340, ORT7341, and ANT1902. All the alleles contain 13 motifs. * indicates incompletely digested DNA. Analysis was done as in Fig​Fig11B. Graphic representation of the instability measurement of central loop length CEB25 variants in WT cells treated with Phen-DC3 (left panel) and inpif1Δ cells (right panel). Instability is inversely correlated to the central loop length in both contexts (two-tailed Spearman correlation test). Alleles bearing sequence modifications other than the central loop (side loops, or intervening sequence) have not been plotted.[2]. Aurèle Piazza, et al. Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites. EMBO J. 2015 Jun 12; 34(12): 1718–1734
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