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Xylene Cyanol

MacsChem > Biological Stains > Xylene Cyanol

What is Xylene Cyanol?

Xylene Cyanol is a synthetic anionic triarylmethane dye. It is characterized by its distinctive blue-green color and high water solubility. Under electrophoretic conditions, the dye is negatively charged and can therefore migrate towards the anode in an electric field. Its consistent migration behavior and excellent visibility are ideal for laboratory staining and analytical procedures. Owing to its consistent physicochemical properties, it is commonly incorporated into laboratory formulations used for electrophoretic and biochemical analyses.

Structure of Xylene Cyanol

CAS No.: 2650-17-1

Synonyms:  Acid blue 147, Cyanol FF, XC, Xylene Cyanole FF

Properties of Xylene Cyanol

Physical Properties
Chemical formulaC25H27N2NaO6S2
IUPAC Name

sodium 4-[(Z)-[4-(ethylamino)-3-methylphenyl]-(4-ethylimino-3-

methylcyclohexa-2,5-dien-1-ylidene)methyl]-6-hydroxybenzene-1,3-disulfonic acid 

Molecular weight555.6 g/mol
SolubilitySoluble in water
AppearanceCrystalline Powder
StorageStore at Room Temperature
Chemical Properties
ColorGreen
Physical StateSolid
Melting Point295° C
λmax613 – 616 nm
OdorOdorless

Applications of Xylene Cyanol

  • Gel Electrophoresis Tracking: Xylene Cyanol is widely used as a tracking dye in agarose and polyacrylamide gel electrophoresis (PAGE). The predictable electrophoretic mobility enables researchers to visually monitor the migration of nucleic acids and to determine when the electrophoretic separation is complete.
  • Loading Buffer Formulation: It is commonly incorporated into DNA and RNA loading buffers. Its unique blue-green color enhances the visibility of the sample while loading and allows continuous monitoring throughout electrophoresis without any interaction with the nucleic acids.
  • Nucleic Acid Analysis: It is used in DNA sequencing workflows and electrophoretic mobility shift assays (EMSA), including studies involving single-stranded DNA (ssDNA), where it serves as a reliable migration marker during molecular analysis.
  • Analytical & Biochemical Research: It is used in spectrophotometric methods for sensitive determination of platinum(IV) and chromium ions. It is also used to study the interaction of dyes with biomolecules, contributing to the development of improved analytical methods and staining procedures.
  • Special Research Applications: It is used as a pH indicator and in laboratory color standards. It has also been studied in experimental biomedical research, such as the study of dye-inactivated Sendai virus vaccines.
Pictograms :Warning pictogram
Hazard Statements :

H319: Causes serious eye irritation

Precautionary statements :

P264: Wash thoroughly after handling. 

P280: Wear protective gloves/protective clothing/eye protection/face protection. 

P337+P313: If eye irritation persists: Get medical advice/attention. 

P305+P351+P338: IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing

 

What is Xylene Cyanol?

Xylene Cyanol is a synthetic anionic triarylmethane dye. It is characterized by its distinctive blue-green color and high water solubility. Under electrophoretic conditions, the dye is negatively charged and can therefore migrate towards the anode in an electric field. Its consistent migration behavior and excellent visibility are ideal for laboratory staining and analytical procedures. Owing to its consistent physicochemical properties, it is commonly incorporated into laboratory formulations used for electrophoretic and biochemical analyses.

Structure of Xylene Cyanol

CAS No.: 2650-17-1

Synonyms:  Acid blue 147, Cyanol FF, XC, Xylene Cyanole FF

Properties of Xylene Cyanol

Physical Properties
Chemical formulaC25H27N2NaO6S2
IUPAC Name

sodium 4-[(Z)-[4-(ethylamino)-3-methylphenyl]-(4-ethylimino-3-

methylcyclohexa-2,5-dien-1-ylidene)methyl]-6-hydroxybenzene-1,3-disulfonic acid 

Molecular weight555.6 g/mol
SolubilitySoluble in water
AppearanceCrystalline Powder
StorageStore at Room Temperature
Chemical Properties
ColorGreen
Physical StateSolid
Melting Point295° C
λmax613 – 616 nm
OdorOdorless

Applications of Xylene Cyanol

  • Gel Electrophoresis Tracking: Xylene Cyanol is widely used as a tracking dye in agarose and polyacrylamide gel electrophoresis (PAGE). The predictable electrophoretic mobility enables researchers to visually monitor the migration of nucleic acids and to determine when the electrophoretic separation is complete.
  • Loading Buffer Formulation: It is commonly incorporated into DNA and RNA loading buffers. Its unique blue-green color enhances the visibility of the sample while loading and allows continuous monitoring throughout electrophoresis without any interaction with the nucleic acids.
  • Nucleic Acid Analysis: It is used in DNA sequencing workflows and electrophoretic mobility shift assays (EMSA), including studies involving single-stranded DNA (ssDNA), where it serves as a reliable migration marker during molecular analysis.
  • Analytical & Biochemical Research: It is used in spectrophotometric methods for sensitive determination of platinum(IV) and chromium ions. It is also used to study the interaction of dyes with biomolecules, contributing to the development of improved analytical methods and staining procedures.
  • Special Research Applications: It is used as a pH indicator and in laboratory color standards. It has also been studied in experimental biomedical research, such as the study of dye-inactivated Sendai virus vaccines.
Pictograms :Warning pictogram
Hazard Statements :

H319: Causes serious eye irritation

Precautionary statements :

P264: Wash thoroughly after handling. 

P280: Wear protective gloves/protective clothing/eye protection/face protection. 

P337+P313: If eye irritation persists: Get medical advice/attention. 

P305+P351+P338: IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing

 

FAQ's

Xylene Cyanol is primarily used as a tracking dye in agarose and polyacrylamide gel electrophoresis. It enables researchers to visually monitor the migration of nucleic acids during electrophoretic separation.

Xylene Cyanol serves as a migration marker and enables researchers to track the progress of electrophoresis. Its predictable mobility helps determine when DNA or RNA fragments have migrated an appropriate distance through the gel.

Xylene Cyanol is also used in spectrophotometric assays, dye-biomolecule interaction studies, pH indicator formulations, and other analytical and biochemical research applications beyond electrophoresis.

Bromophenol Blue and Xylene Cyanol are both synthetic dyes commonly used as tracking dyes in gel electrophoresis. However, they migrate through the gel at different rates. The dual-dye combination provides multiple reference points for easier monitoring of electrophoresis over a wider range of nucleic acid fragment sizes.

Xylene Cyanol is widely used as a tracking dye in both agarose and polyacrylamide gel electrophoresis (PAGE). It helps monitor the migration of DNA and RNA during electrophoresis and is compatible with a wide range of molecular biology applications. 

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