Bisbenzimide HCl
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MedKoo CAT#: 329485

CAS#: 23491-45-4 (HCl)

Description: Bisbenzimide, also known as Pibenzimol, Hoechst 33258, is a cell-permeable, benzimidazole dye that binds to the minor groove of double stranded DNA with preference for adenine and thymine-rich sequences.


Chemical Structure

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Bisbenzimide HCl
CAS# 23491-45-4 (HCl)

Theoretical Analysis

MedKoo Cat#: 329485
Name: Bisbenzimide HCl
CAS#: 23491-45-4 (HCl)
Chemical Formula: C25H27Cl3N6O
Exact Mass: 0.00
Molecular Weight: 533.882
Elemental Analysis: C, 56.24; H, 5.10; Cl, 19.92; N, 15.74; O, 3.00

Price and Availability

Size Price Availability Quantity
100mg USD 550 2 weeks
200mg USD 950 2 weeks
500mg USD 1650 2 weeks
1g USD 2650 2 weeks
2g USD 4650 2 weeks
5g USD 6950 2 weeks
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Related CAS #: 23491-44-3 (free base)   23491-45-4 (HCl)    

Synonym: Bisbenzimide; Bisbenzimide trihydrochloride; Pibenzimol; Pibenzimol HCl; Pibenzimol trihydrochloride. H 33258; HOE 33258; Hoechst 33258; NSC 322921.

IUPAC/Chemical Name: 4-[6-(4-methyl-1-piperazinyl)[2,6'-bi-1H-benzimidazol]-2'-yl]-phenol, trihydrochloride

InChi Key: SMNPLAKEGAEPJD-UHFFFAOYSA-N

InChi Code: 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

SMILES Code: OC1=CC=C(C2=NC3=CC=C(C4=NC5=CC=C(N6CCN(C)CC6)C=C5N4)C=C3N2)C=C1.[H]Cl.[H]Cl.[H]Cl

Appearance: Solid powder

Purity: >98% (or refer to the Certificate of Analysis)

Shipping Condition: Shipped under ambient temperature as non-hazardous chemical. This product is stable enough for a few weeks during ordinary shipping and time spent in Customs.

Storage Condition: Dry, dark and at 0 - 4 C for short term (days to weeks) or -20 C for long term (months to years).

Solubility: Soluble in DMSO

Shelf Life: >2 years if stored properly

Drug Formulation: This drug may be formulated in DMSO

Stock Solution Storage: 0 - 4 C for short term (days to weeks), or -20 C for long term (months).

HS Tariff Code: 2934.99.9001

More Info: Related CAS# 23491-44-3 (free base) 23491-45-4 (trihydrochloride)

Biological target:
In vitro activity:
In vivo activity:

Preparing Stock Solutions

The following data is based on the product molecular weight 533.88 Batch specific molecular weights may vary from batch to batch due to the degree of hydration, which will affect the solvent volumes required to prepare stock solutions.

Recalculate based on batch purity %
Concentration / Solvent Volume / Mass 1 mg 5 mg 10 mg
1 mM 1.15 mL 5.76 mL 11.51 mL
5 mM 0.23 mL 1.15 mL 2.3 mL
10 mM 0.12 mL 0.58 mL 1.15 mL
50 mM 0.02 mL 0.12 mL 0.23 mL
Formulation protocol:
In vitro protocol:
In vivo protocol:

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1: Sakamoto T, Hasegawa D, Fujimoto K. Fluorine-modified bisbenzimide derivative as a molecular probe for bimodal and simultaneous detection of DNAs by (19)F NMR and fluorescence. Chem Commun (Camb). 2015 May 25;51(42):8749-52. doi: 10.1039/c5cc01995h. PubMed PMID: 25873342.

2: Sakamoto T, Hasegawa D, Fujimoto K. Simultaneous detection of single-nucleotide polymorphisms in a DNA bulge structure using a fluorine-modified bisbenzimide derivative. Analyst. 2016 Feb 21;141(4):1214-7. doi: 10.1039/c5an02389k. PubMed PMID: 26661831.

3: Kittimongkolsuk P, Tencomnao T, Santiyanont R. Semi-quantitative detection of gene expression using bisbenzimide dye. Genet Mol Res. 2011 Nov 22;10(4):3747-59. doi: 10.4238/2011.November.22.8. PubMed PMID: 22179998.

4: Tran-Nguyen LT, Schneider B. Cesium chloride-bisbenzimide gradients for separation of phytoplasma and plant DNA. Methods Mol Biol. 2013;938:381-93. doi: 10.1007/978-1-62703-089-2_32. PubMed PMID: 22987432.

5: Ikeda M, Nakagawa H, Suzuki T, Miyata N. Novel bisbenzimide-nitroxides for nuclear redox imaging in living cells. Bioorg Med Chem Lett. 2012 Mar 1;22(5):1949-52. doi: 10.1016/j.bmcl.2012.01.042. PubMed PMID: 22306124.

6: Landex NL, Kayser L. Optimization of an Acridine Orange-bisbenzimide procedure for the detection of apoptosis-associated fluorescence colour changes in etoposide-treated cell cultures. J Mol Histol. 2004 Feb;35(2):133-9. PubMed PMID: 15328917.

7: Iwashita Y, Crang AJ, Blakemore WF. Redistribution of bisbenzimide Hoechst 33342 from transplanted cells to host cells. Neuroreport. 2000 Apr 7;11(5):1013-6. PubMed PMID: 10790874.

8: Demkin VV, Edelstein MV, Zimin AL, Edelstein IA, Suvorov MM. Detection of sequence variation in PCR-amplified fragments of omp2 gene from three species of the family Chlamydiaceae using agarose gel electrophoresis containing bisbenzimide-PEG. FEMS Microbiol Lett. 2000 Mar 15;184(2):215-8. PubMed PMID: 10713423.

9: Müller M, Kruse L, Tabrett AM, Barbara DJ. Detection of a single base exchange in PCR-amplified DNA fragments using agarose gel electrophoresis containing bisbenzimide-PEG. Nucleic Acids Res. 1997 Dec 15;25(24):5125-6. PubMed PMID: 9396825; PubMed Central PMCID: PMC147133.

10: Laube U, Kiderlen AF. Detection of parasites with DNA-binding bisbenzimide H33258 in Pneumocystis carinii- and Leishmania-containing materials. Parasitol Res. 1998 Jul;84(7):559-64. PubMed PMID: 9694372.

11: Laube U, Kiderlen AF. Detection of Pneumocystis carinii with DNA-binding bisBenzimide 33258 Hoechst. J Eukaryot Microbiol. 1997 Nov-Dec;44(6):35S. PubMed PMID: 9508423.

12: Schnell SA, Wessendorf MW. Bisbenzimide: a fluorescent counterstain for tissue autoradiography. Histochem Cell Biol. 1995 Feb;103(2):111-4. PubMed PMID: 7543364.

13: Karlovsky P, de Cock AW. Buoyant density of DNA-Hoechst 33258 (bisbenzimide) complexes in CsCl gradients: Hoechst 33258 binds to single AT base pairs. Anal Biochem. 1991 Apr;194(1):192-7. PubMed PMID: 1714251.

14: Young SD, Hill RP. Radiation sensitivity of tumour cells stained in vitro or in vivo with the bisbenzimide fluorochrome Hoechst 33342. Br J Cancer. 1989 Nov;60(5):715-21. PubMed PMID: 2478182; PubMed Central PMCID: PMC2247311.

15: Bergström I, Heinänen A, Salonen K. Comparison of acridine orange, acriflavine, and bisbenzimide stains for enumeration of bacteria in clear and humic waters. Appl Environ Microbiol. 1986 Mar;51(3):664-7. PubMed PMID: 16347028; PubMed Central PMCID: PMC238937.

16: Andersen O, Rønne M. Effects of ethidium bromide and bisbenzimide (Hoechst 33258) on human lymphocyte chromosome structure. Hereditas. 1986;105(2):269-72. PubMed PMID: 2434451.

17: Bean B, Fogle TA, Gates RD. Rapid staining for the sperm penetration assay using a bisbenzimide dye. Fertil Steril. 1991 Jan;55(1):214-6. PubMed PMID: 1702740.

18: Jin R, Breslauer KJ. Characterization of the minor groove environment in a drug-DNA complex: bisbenzimide bound to the poly[d(AT)].poly[d(AT)]duplex. Proc Natl Acad Sci U S A. 1988 Dec;85(23):8939-42. PubMed PMID: 2461559; PubMed Central PMCID: PMC282622.

19: Hernández LF, Palmer JH. Fluorescent staining of primary plant cell walls using bisbenzimide (33258 Hoechst) fluorochrome. Stain Technol. 1988 May;63(3):190-2. PubMed PMID: 2459818.

20: Portugal J, Waring MJ. Assignment of DNA binding sites for 4',6-diamidine-2-phenylindole and bisbenzimide (Hoechst 33258). A comparative footprinting study. Biochim Biophys Acta. 1988 Feb 28;949(2):158-68. PubMed PMID: 2449244.