BODIPY TR methyl ester is a GFP lipophilic counterstain. BODIPY TR methyl ester readily permeates cell membranes and localizes in intramembranous organelles but does not localize strongly in the plasma membrane. BODIPY TR methyl ester is a better red fluorescent vital stain (Ex=568 nm, Em=625 nm), which may be utilized to reveal the position and shape of cell nuclei, the shape of cells in embryonic tissue, and the organ-forming tissue within the entire embryo border.

Physicochemical Properties

Molecular Formula	C22H17BF2N2O3S
Molecular Weight	438.2548
Exact Mass	438.102
CAS #	150152-63-9
PubChem CID	25164039
Appearance	Typically exists as solid at room temperature
Hydrogen Bond Donor Count	0
Hydrogen Bond Acceptor Count	7
Rotatable Bond Count	6
Heavy Atom Count	31
Complexity	826
Defined Atom Stereocenter Count	0
SMILES	S1C([H])=C([H])C([H])=C1C1C([H])=C([H])C2=C([H])C3=C([H])C([H])=C(C4C([H])=C([H])C(=C([H])C=4[H])OC([H])([H])C(=O)OC([H])([H])[H])N3[B-]([N+]2=1)(F)F
InChi Key	HQMDVGPFFTVIIE-UHFFFAOYSA-N
InChi Code	InChI=1S/C22H17BF2N2O3S/c1-29-22(28)14-30-18-8-4-15(5-9-18)19-10-6-16-13-17-7-11-20(21-3-2-12-31-21)27(17)23(24,25)26(16)19/h2-13H,14H2,1H3
Chemical Name	methyl 2-[4-(2,2-difluoro-12-thiophen-2-yl-3-aza-1-azonia-2-boranuidatricyclo[7.3.0.03,7]dodeca-1(12),4,6,8,10-pentaen-4-yl)phenoxy]acetate
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
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

ln Vitro	Advice (This is our suggested protocol, which should be adjusted to suit your particular circumstances as it simply offers guidance). Procedure for vital staining[1]: 1. To create a 5 mM stock solution, dissolve in anhydrous DMSO. 2. To create a final labeling solution of 100 μM BODIPY TR Methyl Ester Dye containing 2% DMSO, dilute the DMSO stock solution 1:50 into embryonic culture medium (ERM) buffered with 5 mM HEPES (pH 7.2). Keep in storage at -20°C. 3. After being stained for an hour with 100 μM BODIPY TR methyl ester dye, the embryos were rinsed three times with HEPES-buffered ERM. 4. For imaging, place the embryos in an exposed chamber. Live-stained embryos were deyolked and placed onto coverslips for time-lapse recordings. 5. For fixation experiments, embryos were placed for confocal imaging after being fixed for an hour at 4°C in 4% paraformaldehyde in HEPES-buffered ERM. They were then rinsed in ERM. 6. Examine samples using a confocal microscope equipped with an air-cooled Ar-Kr laser and a 640 x 480 pixel frame buffer. Co-excite GFP and BODIPY TR A using the 488 and 568 ester dye wavelengths from the main Ar-Kr laser line. nm) simultaneously.
References	[1]. Visualizing morphogenesis in transgenic zebrafish embryos using BODIPY TR methyl ester dye as a vital counterstain for GFP. Dev Dyn. 2005 Feb;232(2):359-68.
Additional Infomation	BODIPY TR methyl ester is a BODIPY dye and a methyl ester. It has a role as a fluorochrome. It is functionally related to a 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene.

Solubility Data

Solubility (In Vitro)

May dissolve in DMSO (in most cases), if not, try other solvents such as H2O, Ethanol, or DMF with a minute amount of products to avoid loss of samples

Solubility (In Vivo)

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. Injection Formulations (e.g. IP/IV/IM/SC) 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). 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) Oral Formulations 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). 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 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.  (Please use freshly prepared in vivo formulations for optimal results.)

Preparing Stock Solutions		1 mg	5 mg	10 mg
	1 mM	2.2818 mL	11.4090 mL	22.8180 mL
	5 mM	0.4564 mL	2.2818 mL	4.5636 mL
	10 mM	0.2282 mL	1.1409 mL	2.2818 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.