Pyronin Y (C.I.45005) - Biological stain , CAS No.92-32-0

CAS: 92-32-0 Cat. No.: P100851 Molecular Weight: 302.81 EC Number: 202-147-8

GRADE & PURITY Biological Stain

Synonyms

tetramethyldiaminoxanthylium chloride | MFCD00011725 | NSC10454 | NSC-10454 | Pyronin Y, certified by the Biological Stain Commission, Dye content 50 % | W659G165T1 | AI3-52862 | Tetramethyl pyronin | Xanthylium, 3,6-bis(dimethylamino)-, chloride | AMMONI

Storage

Protected from light,Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

Pyronin Y is a dye that intercalates and stains RNA red, and has been shown to accumulate in the mitochondria of viable cells. Multidrug-resistant (MDR) Acinetobacter baumannii studies tested inhibition of the efflux pump by measuring the intracellluar accumulation of Pyronin Y and Ethidium bromide. Research shows that at low Pyronin Y concentrations the cytostatic effect is cell arrest in the G1 phase, whereas at high concentrations the cells arrest is in the G2 and S phase. Pyronin Y has been used in combination with Alcian Blue to asses and study pulmonary diseases, and in combination with Methyl Green to stain nucleic acids in paraffin sections. Additionally Pyronin Y has been used to measure RNA in flow cytometry.
Used in Unna-Pappenheim stain to demonstrate RNA (red) in contrast to DNA (green). Also used for bacteria staining.

Specifications

Synonyms

tetramethyldiaminoxanthylium chloride | MFCD00011725 | NSC10454 | NSC-10454 | Pyronin Y, certified by the Biological Stain Commission, Dye content 50 % | W659G165T1 | AI3-52862 | Tetramethyl pyronin | Xanthylium, 3, 6-bis(dimethylamino)-, chloride | AMMONI

Specifications & Purity

Biological stain

Biochemical and Physiological Mechanisms

Cationic dye that intercalates RNA and is visible as a red band during electrophoresis. Shown to accumulate in the mitochondria of viable cells. At low concentrations the cytostatic effect is cell arrest in the G1 phase

Storage

Protected from light, Store at -20°C

Shipped In

Ice chest + Ice pads

This product requires cold chain shipping. Ground and other economy services are not available.

Grade

Biological Stain

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: 504751244
• Pubchem Sid Url: https://pubchem.ncbi.nlm.nih.gov/substance/504751244
• Canonical Smiles: CN(C)C1=CC2=C(C=C1)C=C3C=CC(=[N+](C)C)C=C3O2.[Cl-]
• IUPAC Name: [6-(dimethylamino)xanthen-3-ylidene]-dimethylazanium;chloride
• InChIKey: INCIMLINXXICKS-UHFFFAOYSA-M
• INCHI: 1S/C17H19N2O.ClH/c1-18(2)14-7-5-12-9-13-6-8-15(19(3)4)11-17(13)20-16(12)10-14;/h5-11H,1-4H3;1H/q+1;/p-1
• Isomeric SMILES: CN(C)C1=CC2=C(C=C1)C=C3C=CC(=[N+](C)C)C=C3O2.[Cl-]
• WGK Germany: 3
• Molecular Weight: 302.81
• Reaxy-Rn: 3795789
• Reaxys-RN_link_address: https://www.reaxys.com/reaxys/secured/hopinto.do?context=S&query=IDE.XRN=3795789&ln=

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Organoheterocyclic compounds
    • Class Benzopyrans
      • Subclass 1-benzopyrans
        • Level5 Dibenzopyrans
          • Level6 Xanthenes

• Kingdom: Organic compounds
• Superclass: Organoheterocyclic compounds
• Class: Benzopyrans
• Subclass: 1-benzopyrans
• Intermediate Tree Nodes: Dibenzopyrans
• Direct Parent: Xanthenes
• Alternative Parents: Dialkylarylamines Benzenoids Heteroaromatic compounds Oxacyclic compounds Organopnictogen compounds Organooxygen compounds Organic chloride salts Hydrocarbon derivatives
• Molecular Framework: Aromatic heteropolycyclic compounds
• Substituents: Xanthene - Tertiary aliphatic/aromatic amine - Dialkylarylamine - Benzenoid - Heteroaromatic compound - Tertiary amine - Oxacycle - Organic chloride salt - Hydrocarbon derivative - Organic salt - Organopnictogen compound - Organic oxygen compound - Organic nitrogen compound - Organooxygen compound - Organonitrogen compound - Amine - Aromatic heteropolycyclic compound
• Description: This compound belongs to the class of organic compounds known as xanthenes. These are polycyclic aromatic compounds containing a xanthene moiety, which consists of two benzene rings joined to each other by a pyran ring.
• External Descriptors: organic chloride salt - iminium salt

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

Associated Targets(Human)

VDR Tclin Vitamin D receptor (26531 Activities)

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PTH1R Tclin Parathyroid hormone receptor (47172 Activities)

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TRHR Tclin Thyrotropin-releasing hormone receptor (318 Activities)

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PLK1 Tchem Serine/threonine-protein kinase PLK1 (28605 Activities)

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SMPD1 Tchem Sphingomyelin phosphodiesterase (13561 Activities)

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GLP1R Tclin Glucagon-like peptide 1 receptor (111429 Activities)

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PIN1 Tchem Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (36611 Activities)

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HEK293 (82097 Activities)

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HepG2 (196354 Activities)

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FEN1 Tchem Flap endonuclease 1 (12055 Activities)

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GNAS Tbio Guanine nucleotide-binding protein G(s), subunit alpha (103405 Activities)

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POLK Tbio DNA polymerase kappa (8653 Activities)

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POLI Tchem DNA polymerase iota (116820 Activities)

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POLH Tchem DNA polymerase eta (21678 Activities)

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KDM4A Tchem Lysine-specific demethylase 4A (52245 Activities)

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APEX1 Tchem DNA-(apurinic or apyrimidinic site) lyase (38016 Activities)

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BRCA1 Tchem Breast cancer type 1 susceptibility protein (15908 Activities)

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EHMT2 Tchem Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 (93046 Activities)

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TSG101 Tbio Tumor susceptibility gene 101 protein (2874 Activities)

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TDP1 Tchem Tyrosyl-DNA phosphodiesterase 1 (345557 Activities)

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L3MBTL1 Tchem Lethal(3)malignant brain tumor-like protein 1 (14536 Activities)

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USP2 Tbio Ubiquitin carboxyl-terminal hydrolase 2 (8818 Activities)

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SMAD3 Tchem Mothers against decapentaplegic homolog 3 (68039 Activities)

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EYA2 Tbio Eyes absent homolog 2 (5884 Activities)

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GMNN Tbio Geminin (128009 Activities)

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IDE Tchem Insulin-degrading enzyme (806 Activities)

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RAB9A Tbio Ras-related protein Rab-9A (22488 Activities)

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CBX1 Tbio Chromobox protein homolog 1 (92434 Activities)

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ATAD5 Tbio ATPase family AAA domain-containing protein 5 (122566 Activities)

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APOBEC3G Tchem DNA dC->dU-editing enzyme APOBEC-3G (12481 Activities)

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BAZ2B Tchem Bromodomain adjacent to zinc finger domain protein 2B (56204 Activities)

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ATXN2 Tbio Ataxin-2 (54410 Activities)

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USP1 Tchem Ubiquitin carboxyl-terminal hydrolase 1 (22556 Activities)

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RGS4 Tchem Regulator of G-protein signaling 4 (13867 Activities)

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APAF1 Tchem Apoptotic protease-activating factor 1 (1188 Activities)

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IDH1 Tclin Isocitrate dehydrogenase [NADP] cytoplasmic (40980 Activities)

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APOBEC3F Tbio DNA dC->dU-editing enzyme APOBEC-3F (14861 Activities)

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RAPGEF3 Tchem Rap guanine nucleotide exchange factor 3 (15528 Activities)

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RAPGEF4 Tchem Rap guanine nucleotide exchange factor 4 (11476 Activities)

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CGA Tbio Glycoprotein hormones alpha chain (29278 Activities)

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WRN Tbio Werner syndrome ATP-dependent helicase (8824 Activities)

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TARDBP Tchem TAR DNA-binding protein 43 (40113 Activities)

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Associated Targets(non-human)

Acinetobacter baumannii (41033 Activities)

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Escherichia coli (133304 Activities)

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Plasmodium falciparum (966862 Activities)

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Luciferin 4-monooxygenase (66902 Activities)

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ddn Putative uncharacterized protein (49 Activities)

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TGR Thioredoxin glutathione reductase (28579 Activities)

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NS1 Nonstructural protein 1 (33327 Activities)

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vpr Aberrant vpr protein (14595 Activities)

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Mechanisms of Action

Chemical and Physical Properties

• Solubility: Soluble in water (30 mg/mL), methyl cellosolve (9 mg/mL), and ethanol (3 mg/mL).DMSO : 25 mg/mL (82.56 mM; Need ultrasonic)
• Sensitivity: light sensitive；Moisture sensitive
• Melt Point(°C): 250-260°C
• Molecular Weight: 302.800 g/mol
• Hydrogen Bond Donor Count: 0
• Hydrogen Bond Acceptor Count: 3
• Rotatable Bond Count: 1
• Exact Mass: 302.119 Da
• Monoisotopic Mass: 302.119 Da
• Topological Polar Surface Area: 15.500 Ų
• Heavy Atom Count: 21
• Formal Charge: 0
• Complexity: 480.000
• Isotope Atom Count: 0
• Defined Atom Stereocenter Count: 0
• Undefined Atom Stereocenter Count: 0
• Defined Bond Stereocenter Count: 0
• Undefined Bond Stereocenter Count: 0
• The total count of all stereochemical bonds: 0
• Covalently-Bonded Unit Count: 2

XLogP3

References

1. Mao Xu, Qi Tang, Yuchen Liu, Jiaqi Shi, Weiyu Zhang, Chan Guo, Qiuwen Liu, Weiwei Lei, Cheng Chen.  (2023)  Charged Boron Nitride Nanosheet Membranes for Improved Organic Solvent Nanofiltration.  ACS Applied Materials & Interfaces,      [PMID:36820819] [10.1021/acsami.2c20893]

2. Jing Liang, Qiang Shan, Tianqi Liu, Wenbin Liang, Xin Zhang, Wei Qi, Hongxin Tan, Shaobo Du, Lijuan Qian, Zhan Li, Ximeng Chen.  (2021)  One-step synthesis of annual ring-shaped planar nitrogen/sulfur co-doped nanoporous graphene for supercapacitance.  ELECTROCHIMICA ACTA,      [PMID:] [10.1016/j.electacta.2021.139137]

3. Junmei Fan, Enrui Wu, Jinlong Dong, Ruitao Zhu, Meiqin Li, Jiangning Gao, Hongfei Han, Liping Ding.  (2021)  A minimalist ratiometric fluorescent sensor based on non-covalent ternary platform for sensing H2S in aqueous solution and serum.  COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS,      [PMID:] [10.1016/j.colsurfa.2021.126299]