Xylene Cyanol FF - Suitable for molecular biology , CAS No.2650-17-1

CAS: 2650-17-1 Cat. No.: X105504 Molecular Weight: 538.61 EC Number: 220-167-5 PubChem CID: 23687514

GRADE & PURITY Suitable for molecular biology

Synonyms

Xylene Cyanol FF | Acid blue 147 | Xylene cyanole FF | AMY22431 | MFCD00019481 | XYLENECYANOLFF | 1,3-Benzenedisulfonic acid, 4-[[4-(ethylamino)-3-methylphenyl][4-(ethylimino)-3-methyl-2,5-cyclohexadien-1-ylidene]methyl]-, sodium salt (1:1) | Sodium 4-((4

Storage

Room temperature

Shipped In

Normal

Overview

Xylene cyanol is often used as a tracking dye during agarose or polyacrylamide gel electrophoresis. It has a slight negative charge and will migrate the same direction as DNA, allowing the user to monitor the progress of molecules moving through the gel. The rate of migration varies with gel composition.

Xylene Cyanol FF is used as a:

· histological stain and as tracker dye in DNA sequencing and electrophoresis 

· gel-loading dye

· formamide RNA loading dye

· tracking dye in native polyacrylamide gel electrophoresis (PAGE) loading buffer

Specifications

Synonyms

Xylene Cyanol FF | Acid blue 147 | Xylene cyanole FF | AMY22431 | MFCD00019481 | XYLENECYANOLFF | 1, 3-Benzenedisulfonic acid, 4-[[4-(ethylamino)-3-methylphenyl][4-(ethylimino)-3-methyl-2, 5-cyclohexadien-1-ylidene]methyl]-, sodium salt (1:1) | Sodium 4-((4

Specifications & Purity

Suitable for molecular biology

Biochemical and Physiological Mechanisms

Xylene Cyanol FF acts as nucleic acid stain.Tracking dye commonly used for nucleic acids. Used in both agarose or polyacrylamide gel electrophoresis. It has a slight negative charge and will migrate in the same direction as DNA, allowing the user to monit

Storage

Room temperature

Shipped In

Normal

Grade

Suitable for molecular biology

Note

Wherever possible, you should prepare and use solutions on the same day. However, if you need to make up stock solutions in advance, we recommend that you store the solution as aliquots in tightly sealed vials at -20°C. Generally, these will be useable for up to one month. Before use, and prior to opening the vial we recommend that you allow your product to equilibrate to room temperature for at least 1 hour. Need more advice on solubility, usage and handling? Please visit our frequently asked questions (FAQ) page for more details.

Names and Identifiers

• Pubchem Sid: 488200535
• Pubchem Sid Url: https://pubchem.ncbi.nlm.nih.gov/substance/488200535
• Canonical Smiles: CCNC1=C(C=C(C=C1)C(=C2C=CC(=NCC)C(=C2)C)C3=C(C=C(C=C3)S(=O)(=O)[O-])S(=O)(=O)O)C.[Na+]
• IUPAC Name: sodium;4-[(Z)-[4-(ethylamino)-3-methylphenyl]-(4-ethylimino-3-methylcyclohexa-2,5-dien-1-ylidene)methyl]-3-sulfobenzenesulfonate
• InChIKey: VVLFAAMTGMGYBS-VARVZIDFSA-M
• 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?
• Isomeric 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+]
• WGK Germany: 3
• PubChem CID: 23687514
• Molecular Weight: 538.61

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Benzenoids
    • Class Benzene and substituted derivatives
      • Subclass Diphenylmethanes

• Kingdom: Organic compounds
• Superclass: Benzenoids
• Class: Benzene and substituted derivatives
• Subclass: Diphenylmethanes
• Intermediate Tree Nodes: Not available
• Direct Parent: Diphenylmethanes
• Alternative Parents: Monocyclic monoterpenoids Benzenesulfonic acids and derivatives Aromatic monoterpenoids Benzenesulfonyl compounds 1-sulfo,2-unsubstituted aromatic compounds Phenylalkylamines Aniline and substituted anilines Aminotoluenes Secondary alkylarylamines Sulfonyls Secondary ketimines Organosulfonic acids Azomethines Propargyl-type 1,3-dipolar organic compounds Organopnictogen compounds Organic zwitterions Organic sodium salts Organic oxides Hydrocarbon derivatives Carbonyl compounds
• Molecular Framework: Aromatic homomonocyclic compounds
• Substituents: Diphenylmethane - Benzenesulfonate - Monoterpenoid - Monocyclic monoterpenoid - Aromatic monoterpenoid - Benzenesulfonyl group - 1-sulfo,2-unsubstituted aromatic compound - Arylsulfonic acid or derivatives - Aminotoluene - Phenylalkylamine - Aniline or substituted anilines - Toluene - Secondary aliphatic/aromatic amine - Sulfonyl - Organosulfonic acid - Organosulfonic acid or derivatives - Organic sulfonic acid or derivatives - Secondary ketimine - Azomethine - Organic alkali metal salt - Organic 1,3-dipolar compound - Propargyl-type 1,3-dipolar organic compound - Secondary amine - Organic nitrogen compound - Organic oxygen compound - Organopnictogen compound - Organic oxide - Hydrocarbon derivative - Organic sodium salt - Organic salt - Organic zwitterion - Organosulfur compound - Organonitrogen compound - Carbonyl group - Amine - Aromatic homomonocyclic compound
• Description: This compound belongs to the class of organic compounds known as diphenylmethanes. These are compounds containing a diphenylmethane moiety, which consists of a methane wherein two hydrogen atoms are replaced by two phenyl groups.
• External Descriptors: Not available

Data sources

1. Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS. ClassyFire: Automated Chemical Classification With A Comprehensive, Computable Taxonomy. Journal of Cheminformatics, 2016, 8:61.

DOI: 10.1186/s13321-016-0174-y

Chemical and Physical Properties

• Solubility: Soluble in water.
• Sensitivity: Hygroscopic
• Melt Point(°C): 295°C
• Molecular Weight: 538.600 g/mol
• Hydrogen Bond Donor Count: 2
• Hydrogen Bond Acceptor Count: 8
• Rotatable Bond Count: 7
• Exact Mass: 538.121 Da
• Monoisotopic Mass: 538.121 Da
• Topological Polar Surface Area: 153.000 Ų
• Heavy Atom Count: 36
• Formal Charge: 0
• Complexity: 1120.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 0
• Undefined Atom Stereocenter Count: 0
• Defined Bond Stereocenter Count: 1
• Undefined Bond Stereocenter Count: 0
• The total count of all stereochemical bonds: 1
• Covalently-Bonded Unit Count: 2

XLogP3

References

1. Ting Zeng, Jie Yin, Ziwen Liu, Zhaoxing Li, Yu Zhang, Yang Lv, Mei-Ling Lu, Min Luo, Meirong Chen, Yibei Xiao.  (2023)  Mechanistic insights into transposon cleavage and integration by TnsB of ShCAST system.  Cell Reports,      [PMID:37379212] [10.1016/j.celrep.2023.112698]