Xylene Cyanol FF is an acidic triphenylmethane dye. Xylene Cyanol FF can be used for histochemical staining of hemoglobin peroxidase or as a tracking dye for DNA sequencing in electrophoresis. Xylene Cyanol FF will be catalyzed by Fe and Al to accelerate oxidation when the dual oxidants hydrogen peroxide and potassium periodate are added. Xylene Cyanol FF can thus determine the Fe and Al content in the solution to be tested using spectrophotometry.

Physicochemical Properties

Molecular Formula	C25H27N2NAO6S2
Molecular Weight	538.61
Exact Mass	538.12
CAS #	2650-17-1
PubChem CID	23687514
Appearance	Dark green to black solid powder
Melting Point	295°C
LogP	6.591
Hydrogen Bond Donor Count	2
Hydrogen Bond Acceptor Count	8
Rotatable Bond Count	7
Heavy Atom Count	36
Complexity	1120
Defined Atom Stereocenter Count	0
SMILES	CCNC1=C(C=C(C=C1)/C(=C/2\C=CC(=NCC)C(=C2)C)/C3=C(C=C(C=C3)S(=O)(=O)[O-])S(=O)(=O)O)C.[Na+]
InChi Key	VVLFAAMTGMGYBS-VARVZIDFSA-M
InChi Code	InChI=1S/C25H28N2O6S2.Na/c1-5-26-22-11-7-18(13-16(22)3)25(19-8-12-23(27-6-2)17(4)14-19)21-10-9-20(34(28,29)30)15-24(21)35(31,32)33;/h7-15,26H,5-6H2,1-4H3,(H,28,29,30)(H,31,32,33);/q;+1/p-1/b25-19-,27-23?;
Chemical Name	sodium;4-[(Z)-[4-(ethylamino)-3-methylphenyl]-(4-ethylimino-3-methylcyclohexa-2,5-dien-1-ylidene)methyl]-3-sulfobenzenesulfonate
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 (e.g. under nitrogen), avoid exposure to moisture and light.
Shipping Condition	Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)

Biological Activity

ln Vitro

In various polyacrylamide gel electrophoresis methods, Xylene Cyanol FF can trace DNA. The following is the operation [1]: 1. applied when denaturing gel. (1) To make the gel, combine 8.3 M urea with 10% acrylamide (19:1, acrylamide:bisacrylamide). 55°C is the usage temperature. Prepare the electrophoresis buffer (TBE) by mixing 89 mM Tris, HCl, pH 8.0, 89 mM boric acid, and 2 mM EDTA. (3) Ready the loading buffer: 0.1% Xylene Cyanol FF, 1 mM EDTA, and 10 mM NaOH. (4) The gel was run at 60 °C (31 V/cm, constant voltage) on a Hoefer SE 600 electrophoresis device or at 70 W (50 V/cm, constant power) on an IBI model STS 45 electrophoresis device. (5) Apply X-ray film to the gel after it has dried on Whatman 3MM paper. Up to 15 hours of exposure are allowed. 2. applied when denaturing gels. Gel should be prepared with 8% acrylamide (19:1, acrylamide:bisacrylamide). Prepare the DNA suspension by adding 12.5 mM magnesium acetate (TAEMg), 20 mM acetic acid, 2 mM EDTA, 40 mM Tris²HCl, pH 8.0, and these ingredients. Bring the suspension of DNA to a boil and then gradually let it cool down to 16 °C. Create a staining solution by mixing 50% glycerol, 0.02% bromophenol blue, 0.02% Xylene Cyanol FF, and TAEMg. Use this solution to dilute the sample until it reaches a final volume of 10 µL. (5) The gel was electrophoresed at 11 V/cm at 16 °C using a Hoefer SE-600 gel electrophoresis apparatus. It was then exposed to X-ray film for a maximum of 15 hours or stained with Stainsall dye.

References

[1]. Antiparallel DNA double crossover molecules as components for nanoconstruction. Journal of the American Chemical Society, 1996, 118(26): 6131-6140. [2]. Determination of iron and aluminum based on the catalytic effect on the reaction of xylene cyanol FF with hydrogen peroxide and potassium periodate. Journal of the Brazilian Chemical Society, 2011, 22: 1987-1992.

Solubility Data

Solubility (In Vitro)

May dissolve in DMSO (in most cases), if not, try other solvents such as H2O, Ethanol, or DMF with a minute amount of products to avoid loss of samples

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 : 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). 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 : PEG300：Tween 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). 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	1.8566 mL	9.2832 mL	18.5663 mL
	5 mM	0.3713 mL	1.8566 mL	3.7133 mL
	10 mM	0.1857 mL	0.9283 mL	1.8566 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.