HOE 33342, formerly known as Hoechst 33342, HO342, is a Benzimidazole fluorescent dye and a Cell permeable fluorescent DNA stain; binds minor groove of AT-rich regions. HOE 33342 trihydrochlorde is used to quantify DNA in viable cells.

Physicochemical Properties

Molecular Formula	C27H28N6O
Molecular Weight	452.5508
Exact Mass	452.232
Elemental Analysis	C, 71.66; H, 6.24; N, 18.57; O, 3.54
CAS #	23491-52-3
Related CAS #	Hoechst 33342 trihydrochloride;875756-97-1;Hoechst 33342 analog;178481-68-0;Hoechst 33342 analog 2;106050-84-4
PubChem CID	1464
Appearance	Brown to breen solid powder
Melting Point	268ºC
LogP	7.139
Hydrogen Bond Donor Count	2
Hydrogen Bond Acceptor Count	5
Rotatable Bond Count	5
Heavy Atom Count	34
Complexity	664
Defined Atom Stereocenter Count	0
InChi Key	PRDFBSVERLRRMY-UHFFFAOYSA-N
InChi Code	InChI=1S/C27H28N6O/c1-3-34-21-8-4-18(5-9-21)26-28-22-10-6-19(16-24(22)30-26)27-29-23-11-7-20(17-25(23)31-27)33-14-12-32(2)13-15-33/h4-11,16-17H,3,12-15H2,1-2H3,(H,28,30)(H,29,31)
Chemical Name	2-(4-ethoxyphenyl)-6-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-benzimidazole
Synonyms	HO342; HOE33342; HO 342; HOE-33342; HO-342; Bisbenzimide; HOE 33342; Hoechst 33342
HS Tariff Code	2934.99.9001
Storage	Powder-20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month Note: This product requires protection from light (avoid light exposure) during transportation and storage.
Shipping Condition	Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)

Biological Activity

Targets	Dye reagent；DNA Stain
ln Vitro	1. Preparation of Hoechst working solution 1.1: Preparation of Hoechst stock solution. Prepare 1 mg/mL Hoechst stock solution using DMSO. *Note: After aliquot, Hoechst stock solution should be stored in the dark (protect from light) at -4°C or -20°C. 1.2: Preparing working solution: Dilute the stock solution with PBS or a serum-free cell culture medium to a 10 μg/mL of Hoechst working solution. *Note: Before use, please make sure that the Hoechst working solution concentration is appropriate for your experiments, and use freshly prepared working solution for optimal results. 2. Staining (Suspended cells) 2.1: Centrifuge cells, add PBS, then wash twice for five minutes each time, or until the cell density reaches 1×106/mL. 2.2: Add 1 mL of Hoechst working solution and let it settle for 3–10 minutes. 2.3: Centrifuge for 3–4 minutes at 400 g, then discard supernatants. 2.4: Wash the cells twice with PBS, five minutes each time. 2.5: Re-suspend the cells in 1 mL of PBS or serum-free media, and use a flow cytometer or fluorescence microscope to observe. 3. Staining (Adherent cell) 3.1: Grow adherent cells on sterile coverslips. 3.2: Remove the cover glass from the culture medium and remove excess culture medium. 3.3: Add 100 μ L of dye working solution, gently shake to completely cover the cells, and incubate for 3-10 minutes. 3.4: Remove the dye working solution, wash 2-3 times with culture medium for 5 minutes each time, and observe using a fluorescence microscope or flow cytometer. Note 1. Please adjust the concentration of Hoechst working solution according to the actual situation and prepare it for use. 2. This product is limited to the scientific research use of professional researchers and cannot be used for clinical diagnosis, treatment, food or medicine. For your safety and health, please wear laboratory clothes and disposable gloves when operating.
Enzyme Assay	Hoechst 33342 binds to adenine-thymine-rich regions of DNA in the minor groove. On binding to DNA, the fluorescence greatly increases. This protocol describes the use of Hoechst 33342 to label nuclear DNA of cells grown in culture. Hoechst 33342 can also be used to stain fixed cells by substituting Hoechst 33342 for DAPI.[1] Hoechst 33342 can also be used to stain fixed cells by substituting Hoechst 33342 for DAPI in the protocol described in Labeling Nuclear DNA Using DAPI (Chazotte 2011a). Autofluorescence from endogenous cellular molecules such as the reduced forms of nicotinamide adenine dinucleotide or flavin adenine dinucleotide can interfere with imaging by reducing the signal-to-noise ratio. This occurs when the excitation and/or emission wavelengths of the probe and the autofluorescing molecules are similar, e.g., frequently with excitation wavelengths <500 nm, and particularly at ultraviolet wavelengths. Autofluorescence can be reduced by careful selection of the excitation and the emission wavelengths used, by treating fixed cells with reducing agents (e.g., a 1% solution of sodium borohydride [NaBH4] for 20 min), and by comparing the experimental images with unlabeled control slides. Avoid fixation with glutaraldehyde, because it can increase interference from cellular autofluorescence, most frequently at wavelengths <500 nm.[1] This protocol assumes that the cells of interest were grown on glass microscope coverslips immersed in small Petri dishes containing culture medium. Generally, labeling conditions vary by cell type, and it might be necessary to alter the protocol for a particular use. To mount cells labeled using the technique described here, see Mounting Live Cells onto Microscope Slides (Chazotte 2011b).[3] A number of fluorescent stains are available that label DNA and allow easy visualization of the nucleus in interphase cells and chromosomes in mitotic cells. One advantage of Hoechst 33342 is that it is membrane permeant and, thus, can stain live cells. Hoechst 33342 binds to adenine-thymine-rich regions of DNA in the minor groove. On binding to DNA, the fluorescence greatly increases. This protocol describes the use of Hoechst 33342 to label nuclear DNA of cells grown in culture.
Cell Assay	Method[1] Do not allow the cells to dry out at any time during the protocol. 1. Dilute the Hoechst stock solution 1:100 in H2O for use in labeling. 2. Aspirate the cell medium from cells grown on coverslips. Rinse the cells three times with PBS+. 3. Incubate the cells in the Hoechst labeling solution (from Step 1) for 10-30 min at room temperature. 4. Aspirate the labeling solution. Rinse the cells three times in PBS+. 5. Mount the coverslips as described in Mounting Live Cells onto Microscope Slides (Chazotte 2011b).
References	[1]. Chazotte B. Labeling nuclear DNA with hoechst 33342. Cold Spring Harb Protoc. 2011 Jan 1;2011(1):pdb.prot5557. [2]. Chazotte B (2011a) Labeling nuclear DNA using DAPI. Cold Spring Harb Protoc doi:10.1101/pdb.prot5556. [3]. Chazotte B (2011b) Mounting live cells onto microscope slides. Cold Spring Harb Protoc doi:10.1101/pdb.prot5554.
Additional Infomation	2'-(4-ethoxyphenyl)-5-(4-methylpiperazin-1-yl)-2,5'-bibenzimidazole is a bibenzimidazole and a N-methylpiperazine. It has a role as a fluorochrome. It is functionally related to a pibenzimol. See also: Bisbenzimide ethoxide trihydrochloride (annotation moved to).

Solubility Data

Solubility (In Vitro)

DMSO : ~6.25 mg/mL (~13.81 mM) H2O : < 0.1 mg/mL

Solubility (In Vivo)

Solubility in Formulation 1: ≥ 0.5 mg/mL (1.10 mM) (saturation unknown) in 10% DMSO + 40% PEG300 + 5% Tween80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 5.0 mg/mL clear DMSO stock solution to 400 μL PEG300 and mix evenly; then add 50 μL Tween-80 to the above solution and mix evenly; then add 450 μL normal saline to adjust the volume to 1 mL. Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH₂ O to obtain a clear solution. Solubility in Formulation 2: ≥ 0.5 mg/mL (1.10 mM) (saturation unknown) in 10% DMSO + 90% (20% SBE-β-CD in Saline) (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 5.0 mg/mL clear DMSO stock solution to 900 μL of 20% SBE-β-CD physiological saline solution and mix evenly. Preparation of 20% SBE-β-CD in Saline (4°C，1 week): Dissolve 2 g SBE-β-CD in 10 mL saline to obtain a clear solution. Solubility in Formulation 3: ≥ 0.5 mg/mL (1.10 mM) (saturation unknown) in 10% DMSO + 90% Corn Oil (add these co-solvents sequentially from left to right, and one by one), clear solution. For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 5.0 mg/mL clear DMSO stock solution to 900 μL of corn oil and mix evenly. Solubility in Formulation 4: 5 mg/mL (11.05 mM) in PBS (add these co-solvents sequentially from left to right, and one by one), clear solution; with ultrasonication (<60°C).  (Please use freshly prepared in vivo formulations for optimal results.)

Preparing Stock Solutions		1 mg	5 mg	10 mg
	1 mM	2.2097 mL	11.0485 mL	22.0970 mL
	5 mM	0.4419 mL	2.2097 mL	4.4194 mL
	10 mM	0.2210 mL	1.1049 mL	2.2097 mL

*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.