Hoechst 33258 staining solution (ready to use) - 5ug/ml in H2O , CAS No.23491-45-4

CAS: 23491-45-4 Cat. No.: H598341 Molecular Weight: 533.90 Beilstein Registry Number: 4088183 EC Number: 245-690-6 PubChem CID: 31953

GRADE & PURITY 5ug/ml in H2O

Storage

Protected from light,Store at -20°C

Shipped In

Ice chest + Ice pads

Overview

​Hoechst 33258, also known as bis benzimide h 33258 or hoe 33258, is a non embedding bright blfluorescent dye. Dyes have weak fluorescence in solution, and their fluorescence becomes bright after binding with DNA at the minor groove in the DNA poly at sequence rich region in living cells. Therefore, such dyes are also known as DNA probes. Because of the low background, the stained cells do not need washing steps, and the staining is very stable, non-toxic to live cells, and can last for several days or longer after combined with DNA staining. Hoechst 33258 has higher solubility in water than Hoechst 33342, but both dyes have high cell membrane permeability and are widely used for apoptosis detection. After staining, it can be observed by fluorescence microscope or detected by flow cytometry. Take adherent cells (96 well plate) as an example, 100 per well μ L staining solution, 10 ml can be used for the staining of 100 wells.

Product parameters：

Ex/em (bound DNA) = 352/461 nm； Ex/Em (unbound DNA) = 346/460 nm

Matters needing attention：

1. please centrifuge the product to the bottom of the tube immediately before use, and then conduct subsequent experiments. 

2. if you need to adjust the concentration, please select H598341 and configure the appropriate working fluid concentration by yourself. 

3. fluorescent dyes have quenching problems. It is recommended to observe immediately after staining live cells or tissues. 

4. for your safety and health, please wear experimental clothes and disposable gloves.

Scope of application：

Nuclear staining

Experimental steps:
1. For fixed cells or tissues
(1) For cell or tissue samples, wash and remove the fixative appropriately after fixation. If immunofluorescence staining is required, first perform immunofluorescence staining, and then follow the subsequent steps to perform Hoechst 33258 staining.
(2) For adherent cells or tissue sections, add a small amount of Hoechst 33258 working solution and cover the sample. For suspended cells, add at least three times the volume of the sample to be tested and mix well. Leave at room temperature for 3-5 minutes.
(3) Remove Hoechst 33258 staining solution and wash 2-3 times with TBST, PBS, or physiological saline for 3-5 minutes each time.
Note: The cleaning steps are optional but not necessary and do not affect dyeing after cleaning.
(4) Observe directly under a fluorescence microscope or observe under a fluorescence microscope after sealing. When a cell undergoes apoptosis, the nucleus of the apoptotic cell can be seen to be densely stained or fragmented and densely stained.
2. For live cells or tissues
(1) Add an appropriate amount of Hoechst 33258 working solution and fully cover the sample to be stained. Typically, 1 mL of staining solution is required per well for a six well plate, and 100 mL is required per well for a 96 well plate μ L's staining solution.
(2) Incubate at room temperature in dark for 10-30 minutes.
(3) Discard the staining solution, wash 2-3 times with PBS, then add 50 μ Perform micrographs using PBS.
Note: The cleaning steps are optional but not necessary and do not affect dyeing after cleaning.

Specifications

Specifications & Purity

5ug/ml in H2O

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.

Names and Identifiers

• Canonical Smiles: CN1CCN(CC1)C2=CC3=C(C=C2)N=C(N3)C4=CC5=C(C=C4)N=C(N5)C6=CC=C(C=C6)O.Cl.Cl.Cl
• IUPAC Name: 4-[6-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-benzimidazol-2-yl]phenol;trihydrochloride
• InChIKey: SMNPLAKEGAEPJD-UHFFFAOYSA-N
• INCHI: 1S/C25H24N6O.3ClH/c1-30-10-12-31(13-11-30)18-5-9-21-23(15-18)29-25(27-21)17-4-8-20-22(14-17)28-24(26-20)16-2-6-19(32)7-3-16;;;/h2-9,14-15,32H,10-13H2,1H3,(H,26,28)(H,27,29);3*1H
• Isomeric SMILES: CN1CCN(CC1)C2=CC3=C(C=C2)N=C(N3)C4=CC5=C(C=C4)N=C(N5)C6=CC=C(C=C6)O.Cl.Cl.Cl
• WGK Germany: 3
• RTECS: SM1140500
• PubChem CID: 31953
• Molecular Weight: 533.90
• Beilstein: 4088183

Taxonomic Classification

Taxonomy Tree

• Kingdom Organic compounds
  • Superclass Organoheterocyclic compounds
    • Class Benzimidazoles
      • Subclass Phenylbenzimidazoles

• Kingdom: Organic compounds
• Superclass: Organoheterocyclic compounds
• Class: Benzimidazoles
• Subclass: Phenylbenzimidazoles
• Intermediate Tree Nodes: Not available
• Direct Parent: Phenylbenzimidazoles
• Alternative Parents: N-arylpiperazines Phenylimidazoles Dialkylarylamines N-methylpiperazines 1-hydroxy-2-unsubstituted benzenoids Benzene and substituted derivatives Heteroaromatic compounds Trialkylamines Azacyclic compounds Organooxygen compounds Hydrochlorides Hydrocarbon derivatives
• Molecular Framework: Aromatic heteropolycyclic compounds
• Substituents: Phenylbenzimidazole - N-arylpiperazine - 2-phenylimidazole - Dialkylarylamine - Tertiary aliphatic/aromatic amine - 1-hydroxy-2-unsubstituted benzenoid - Phenol - N-alkylpiperazine - N-methylpiperazine - Monocyclic benzene moiety - 1,4-diazinane - Benzenoid - Piperazine - Azole - Heteroaromatic compound - Imidazole - Tertiary aliphatic amine - Tertiary amine - Azacycle - Hydrochloride - Organooxygen compound - Organonitrogen compound - Hydrocarbon derivative - Organic oxygen compound - Organic nitrogen compound - Amine - Aromatic heteropolycyclic compound
• Description: This compound belongs to the class of organic compounds known as phenylbenzimidazoles. These are compounds containing a phenylbenzimidazole skeleton, which consists of a benzimidazole moiety where its imidazole ring is attached to a phenyl group.
• 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

Associated Targets(Human)

TOP1 Tclin DNA topoisomerase I (7553 Activities)

Discover Target: TOP1

Activity Type	Relation	Activity value	Units	Action Type	Journal	PubMed Id	doi	Assay Aladdin ID

TOP2A Tclin DNA topoisomerase II alpha (6317 Activities)

Discover Target: TOP2A

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DU-145 (51482 Activities)

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MCF7 (126967 Activities)

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A549 (127892 Activities)

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KG-1 (867 Activities)

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HeLa (62764 Activities)

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Associated Targets(non-human)

Pseudomonas aeruginosa (123386 Activities)

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Enterobacter cloacae (7976 Activities)

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Klebsiella pneumoniae (43867 Activities)

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Shigella flexneri (1836 Activities)

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Staphylococcus aureus (210822 Activities)

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Staphylococcus epidermidis (22802 Activities)

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Acinetobacter baumannii (41033 Activities)

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Citrobacter freundii (1864 Activities)

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Escherichia coli (133304 Activities)

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Enterococcus faecium (13803 Activities)

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Enterococcus faecalis (29875 Activities)

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Calf thymus DNA (4845 Activities)

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Mechanisms of Action

Chemical and Physical Properties

• Melt Point(°C): 314°C
• Molecular Weight: 533.900 g/mol
• Hydrogen Bond Donor Count: 6
• Hydrogen Bond Acceptor Count: 5
• Rotatable Bond Count: 3
• Exact Mass: 532.131 Da
• Monoisotopic Mass: 532.131 Da
• Topological Polar Surface Area: 84.100 Ų
• Heavy Atom Count: 35
• Formal Charge: 0
• Complexity: 634.000
• 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: 4

XLogP3

References

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20. Yanghui Chen, Yuan Li, Junliang Luo, Zixin Li, Yu Huang, Jia Cai, Dongneng Jiang, Defeng Zhang, Jichang Jian, Jun Qiang, Bei Wang.  (2024)  A novel study of brain microvascular endothelial cells induced by astrocyte conditioned medium for constructing blood brain barrier model in vitro: A promising tool for meningitis of teleost.  FISH & SHELLFISH IMMUNOLOGY,      [PMID:38266792] [10.1016/j.fsi.2024.109401]

21. Ouyang Boshu, Shan Caihua, Shen Shun, Dai Xinnan, Chen Qingwang, Su Xiaomin, Cao Yongbin, Qin Xifeng, He Ying, Wang Siyu, Xu Ruizhe, Hu Ruining, Shi Leming, Lu Tun, Yang Wuli, Peng Shaojun, Zhang Jun, Wang Jianxin, Li Dongsheng, Pang Zhiqing.  (2024)  AI-powered omics-based drug pair discovery for pyroptosis therapy targeting triple-negative breast cancer.  Nature Communications,  15  (1): (1-20).  [PMID:39215014] [10.1038/s41467-024-51980-9]

22. Zhang Hongmei, Yang Yunxia, Wang Yanqing.  (2025)  Comprehensive Investigations About the Binding Interactions of Sudan Dyes with DNA by Spectroscopy and Docking Methods.  JOURNAL OF FLUORESCENCE,      [PMID:39777621] [10.1007/s10895-024-04125-6]

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