Dye reagent；DNA Stain
Hoechst 33342 analog 2 trihydrochloride targets DNA by binding to the minor groove. It is also described as a DNA topoisomerase inhibitor. Topoisomerases are enzymes that regulate DNA supercoiling and are essential for DNA replication and transcription. By inhibiting topoisomerase, this compound can interfere with DNA metabolism and exhibit anticancer activity.

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.
In vitro, Hoechst 33342 analog 2 trihydrochloride is used as a fluorescent stain for DNA. Upon binding to DNA, its fluorescence is significantly enhanced. It is used to stain nuclear DNA in live or fixed cells for fluorescence microscopy and flow cytometry. Its reported anticancer activity is also an area of research interest.

Hoechst 33342 analog 2 trihydrochloride is not typically administered as a therapeutic agent in vivo. Its primary use is as a research tool for staining DNA in cellular and molecular biology applications. As a DNA topoisomerase inhibitor, it may have potential for anticancer research, but it is not a clinical drug.

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]

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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.
In vitro assays for Hoechst 33342 analog 2 trihydrochloride are similar to those for other Hoechst dyes. A typical protocol involves preparing a 1 mg/mL stock solution in DMSO, which is then diluted to a working concentration, usually 10 μg/mL, with PBS or serum-free medium. Cells are incubated with the working solution for 3-10 minutes, washed, and then observed under a fluorescence microscope or analyzed by flow cytometry.

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).
Cellular assays using Hoechst 33342 analog 2 trihydrochloride involve incubating live or fixed cells with the dye. For live-cell staining, the dye is added to the culture medium and incubated for a short period. After washing, the cells can be imaged or analyzed. For fixed cells, the staining protocol is similar. The dye's fluorescence is measured using appropriate excitation and emission filters.

Hoechst 33342 analog 2 trihydrochloride is not typically used in animal studies as a drug. Its use in vivo would be limited to research applications where cells are labeled ex vivo and then introduced into the animal for tracking purposes.

Hoechst 33342 analog 2 trihydrochloride has a molecular weight of 659.78 g/mol. It is a small, cell-permeable molecule. Its fluorescence properties are similar to other Hoechst dyes, with excitation and emission maxima in the UV/blue range. As a fluorescent dye, its pharmacokinetics are not a primary concern for its typical in vitro applications.

Hoechst 33342 analog 2 trihydrochloride is generally considered non-toxic at the low concentrations used for DNA staining. However, as a DNA topoisomerase inhibitor, it may have cytotoxic effects at higher concentrations. Standard laboratory safety precautions should be followed when handling the compound. It is for research use only and not for human therapeutic or diagnostic use.

[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.

Cell Staining Example 1: Hoechst 33342 can be used for blue fluorescent staining of cell nuclei. Cell Staining Example 2: Hoechst 33342 can be used for blue fluorescent staining of cell nuclei to detect apoptosis. 1. Stain cells with Hoechst 33342 (10 minutes). 2. Observe using a fluorescence microscope (imaging). Cell Staining Example 3: Hoechst 33342 can be used for blue fluorescent labeling of chromatin. 1. Before imaging, briefly counterstain the chromatin with Hoechst 33342 (5 µg/mL). 2. Observe using a confocal microscope (imaging).
Hoechst 33342 analog 2 trihydrochloride is a fluorescent dye and a DNA topoisomerase inhibitor with anticancer activity. It is an analog of Hoechst 33342 and is used to stain DNA in live or fixed cells for fluorescence microscopy and flow cytometry. Its dual function as a stain and a topoisomerase inhibitor makes it a unique tool for studying DNA biology and cancer.

C25H26CL3IN6O

659.777014255524

658.027

155815-98-8

Hoechst 33342 analog 2;106050-84-4

137195726

Light green to green solid powder

6

5

3

36

677

0

IC1=C(C=CC(=C1)C1=NC2=CC=C(C=C2N1)C1=NC2=CC=C(C=C2N1)N1CCN(C)CC1)O.Cl.Cl.Cl

UMBXUMFHPPBTSO-UHFFFAOYSA-N

InChI=1S/C25H23IN6O.3ClH/c1-31-8-10-32(11-9-31)17-4-6-20-22(14-17)30-25(28-20)16-2-5-19-21(13-16)29-24(27-19)15-3-7-23(33)18(26)12-15;;;/h2-7,12-14,33H,8-11H2,1H3,(H,27,29)(H,28,30);3*1H

2-iodo-4-[6-[6-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-benzimidazol-2-yl]phenol;trihydrochloride

Hoechst-33342 analog 2 trihydrochloride

2934.99.9001

Powder      -20°C    3 years

                     4°C     2 years

In solvent   -80°C    6 months

                  -20°C    1 month

Note: Please store this product in a sealed and protected environment (e.g. under nitrogen), avoid exposure to moisture and light.

Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)

H2O : ~20 mg/mL (~30.31 mM)
DMSO : ~4 mg/mL (~6.06 mM)

Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.

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Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)
*Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution.
Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline)
Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil)
Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals).

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Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)]
*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.
Injection Formulation 5: 2-Hydroxypropyl-β-cyclodextrin : Saline = 50 : 50 (i.e. 500 μL 2-Hydroxypropyl-β-cyclodextrin → 500 μL Saline)
Injection Formulation 6: DMSO : PEG300 : castor oil : Saline = 5 : 10 : 20 : 65 (i.e. 50 μL DMSO → 100 μLPEG300 → 200 μL castor oil → 650 μL Saline)
Injection Formulation 7: Ethanol : Cremophor : Saline = 10： 10 : 80 (i.e. 100 μL Ethanol → 100 μL Cremophor → 800 μL Saline)
Injection Formulation 8: Dissolve in Cremophor/Ethanol (50 : 50), then diluted by Saline
Injection Formulation 9: EtOH : Corn oil = 10 : 90 (i.e. 100 μL EtOH → 900 μL Corn oil)
Injection Formulation 10: EtOH : PEG300：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL EtOH → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline)

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Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium)
Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose
Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals).

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Oral Formulation 3: Dissolved in PEG400
Oral Formulation 4: Suspend in 0.2% Carboxymethyl cellulose
Oral Formulation 5: Dissolve in 0.25% Tween 80 and 0.5% Carboxymethyl cellulose
Oral Formulation 6: Mixing with food powders

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Note: Please be aware that the above formulations are for reference only. InvivoChem strongly recommends customers to read literature methods/protocols carefully before determining which formulation you should use for in vivo studies, as different compounds have different solubility properties and have to be formulated differently.

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 (Please use freshly prepared in vivo formulations for optimal results.)