Created by: Hande Küçük McGinty, Janice Kranz, Joseph Ostrow, Alex Clark, Yu Lin, Saminda Abeyruwan, Uma Vempati, Kunie Sakurai, Vance Lemmon, Ubbo Visser, John Turner, add_name, Stephan Schurer*
Contact: Stephan Schurer stephan dot schurer at med dot miami dot edu
The liquid broth used to grow cells, which is optimized for each cell type and includes additives such as growth factors, buffers, amino acids, antibiotics, etc. This information can be obtained from ATCC or found in relevant publications.
Dimethyl sulfoxide (DMSO) is a common organic solvent that is used to solubilize the chemical compounds prior to their addition to an assay. DMSO can have a significant impact on enzyme activity and the concentration of DMSO in the wells containing compound should be identical to the concentration of DMSO in the control wells. DMSO can also impact the solubility of a compound and its observed potency. Therefore, the concentration of DMSO should be consistent in replicate experiments.
Peptoids are a class of biomimetic polymers based on oligo-N-substituted glycine backbones, designed to mimic peptides and proteins. Peptoids are resistant to proteolysis and not typically denatured by solvent, temperature, or chemical denaturants.
Aptamers are synthetic affinity probes. DNA aptamers are oligonucleotides that bind to a specific target molecule, such as small molecules, proteins, nucleic acids and cells. They are created by selecting them from a large random sequence pool through repeated rounds of in vitro selection.
Aptamers are synthetic affinity probes. Peptide aptamers consist of a variable peptide loop attached at both ends of a protein scaffold, such as thioredoxin-A. They bind to target proteins with high affinity, similar to that of an antibody. They are designed to inhibit the function of other protein inside the cell.
Molecular beacons are hairpin shaped oligonucleotide probes with an internally quenched fluorophore whose fluorescence is restored upon binding to a target nucleic acid. They are used to detect nucleic acids in solution.
The cell culture broth used while performing an assay on cells, which is optimized for each assay type. Some interfering additives such as serum, growth factors, buffers, amino acids, antibiotics, etc. might be eliminated in this medium.
An ionic compound (principally consisting of Na, K, Li, Ca, and Mg as cation) which is used as an additive in an assay.
4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
ethylene glycol ester of luciferin 6' methyl ether
wee1-like protein-luciferin 4-monooxygenase
6,8-difluoro-4-methylumbelliferyl phosphate
PKC inhibitor 3-{1-[3-(dimethylamino)propyl]-1H-indol-3-yl}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione
Brij-35 is a nonionic polyoxyethylene surfactant that is most frequently used as a component of cell lysis buffers or a surfactant in various HPLC applications.
5-Hydroxy-3-(1-methylpiperidin-4-yl)-1H-indole A potent 5-ht1E/1F receptor agonist
CHAPS is a zwitterionic detergent used in the laboratory to solubilize biological macromolecules such as proteins. It is used as a non-denaturing solvent in the process of protein purification and is especially useful in purifying membrane proteins, which are often sparingly soluble or insoluble in aqueous solution due to their native hydrophobicity. CHAPS can also be used in conjunction with nonionic detergents such as Triton X-100.
Cysteine has antioxidant properties due to the ability of thiols to undergo redox reactions.
Dithiothreitol (DTT) is the common name for a small-molecule redox reagent known as Cleland's reagent. DTT's formula is C4H10O2S2 and the molecular structure of its reduced form is shown at the right; its oxidized form is a disulfide-bonded 6-membered ring (shown below). Its name derives from the four-carbon sugar, threose.
5,6,7,13-Tetrahydro-13-methyl-5-oxo-12H-indolo[2,3-a]pyrrolo[3,4-c]carbazole-12-propanenitrile Potent protein kinase C (PKC) inhibitor (IC50 = 7.9 nM).
3-(3,5-Dibromo-4-hydroxy-benzylidene)-5-iodo-1,3-dihydro-indol-2-one Potent, selective and cell-permeable c-Raf1 kinase inhibitor (IC50 = 9 nM). Displays ≥ 100-fold selectivity for raf kinase over CDK1, CDK2, c-src, ERK2, MEK, p38, Tie2, VEGFR2 and c-fm.
An inhibitor of cyclin kinase 2 (CDK2) which prevents and/or reduces the side effects of chemotherapy (alopecia, plantar-palmar syndrome and mucositis).
IGEPAL CA-630 is a nonionic, non-denaturing detergent. Its official IUPAC name is octylphenoxypolyethoxyethanol.
L-(+)-2-Amino-4-phosphonobutyric acid Selective group III metabotropic glutamate receptor agonist.
Lipofectamine™ 2000 Reagent delivers DNA or siRNA with excellent transfection performance for protein expression, gene silencing, and functional assays. Superior efficiency, optimized protocols, and unparalleled success across a broad range of cell lines.
2-(6-(7-Nitrobenz-2-Oxa-1,3-Diazol-4-yl)amino)Hexanoyl-1-Hexadecanoyl-sn-Glycero-3-Phosphocholine (NBD C6-HPC)
NP-40 is a commercially available detergent. The full name of NP-40 is Tergitol-type NP-40, which is nonyl phenoxypolyethoxylethanol.
para-Nitrophenylphosphate (pNPP) is a chromogenic substrate for acid and alkaline phosphatase in ELISA assays. Under their influence the decay to yellow para-nitrophenol is catalysed. This product can be measured with a 405 nm spectrophotometer.
It has the high-energy phosphate bond found (-61.9 kJ/mol) in living organisms, and is involved in glycolysis and gluconeogenesis. In plants, it is also involved in the biosynthesis of various aromatic compounds, and in carbon fixation; in bacteria, it is also used as the source of energy for the phosphotransferase system.
Phosphorylethanolamine or phosphoethanolamine is an ethanolamine derivative that is used to construct sphingomyelins.
Pluronic® F-127 is a nonionic, surfactant polyol (molecular weight approximately 12,500 daltons) that has been found to facilitate the solubilization of water-insoluble dyes and other materials in physiological media.
4-(Dipropylsulfamoyl)benzoic acid Inhibitor of multidrug resistance-associated proteins (MRP).
pyrimidine-4,6-dicarboxylic acid, bis-(4-fluoro-3-methyl-benzylamide) Degrades collagen type I.
Rauwolscine acts predominantly as a α2-adrenergic receptor antagonist. It has also been shown to function as a 5-HT1A receptor partial agonist and 5-HT2A and 5-HT2B receptor antagonist.
4-(3-Butoxy-4-methoxyphenyl)methyl-2-imidazolidone Widely used inhibitor of cyclic nucleotide phosphodiesterase, selective for PDE4 (IC50 = 2.0 μM).
A highly selective and potent non-peptide δ-opioid agonist, 2000-fold selective over μ-opioid receptors. (+)-4-[(αR)-α-((2S,5R)-4-Allyl-2,5-di methyl-1-piperazinyl)-3-methoxybenzyl]-N,N-diethyl benzamide
Sodium orthovanadate is the chemical compound Na3VO4 and contains the tetrahedral VO43−. It is an inhibitor of protein tyrosine phosphatases, alkaline phosphatases and a number of ATPases, most likely acting as a phosphate analogue. The VO43- ion binds reversibly to the active sites of most protein tyrosine phosphatases.
Staurosporine (antibiotic AM-2282 or STS) is a natural product originally isolated in 1977 from the bacterium Streptomyces staurosporeus.
The stibonic acid compound, NSC13778, also know as stibavirin, previously has been reported to inhibit the interaction between transcription factors C/EBP, C/EBPß, CREB, Fos/JunD, and VBP and their cognate DNA sequences, HIV nucleocapsid protein p7 and viral RNA, and HIV gp120 and CD4. Now, we report that this compound is a potent inhibitor of the interaction between transcription factors TFE3, Alveolar Soft Part Sarcoma (ASPS) associated fusion protein ASPL-TFE3 type 1, and ASPL-TFE3 type 2 and their cognate DNA. Proc Amer Assoc Cancer Res, Volume 47, 2006
219479 Cdc2-Like Kinase Inhibitor, TG003 (Z)-1-(3-Ethyl-5-methoxy-2,3-dihydrobenzothiazol-2-ylidene)propan-2-one, Clk Inhibitor, TG003
used for staining of senile amyloid deposits/plaques
Triton X-100 (C14H22O(C2H4O)n) is a nonionic surfactant which has a hydrophilic polyethylene oxide group (on average it has 9.5 ethylene oxide units) and a hydrocarbon lipophilic or hydrophobic group.
Polysorbate 20 (common commercial brand names include Alkest TW 20 and Tween 20) is a polysorbate surfactant whose stability and relative non-toxicity allows it to be used as a detergent and emulsifier in a number of domestic, scientific, and pharmacological applications. It is a polyoxyethylene derivative of sorbitan monolaurate, and is distinguished from the other members in the polysorbate range by the length of the polyoxyethylene chain and the fatty acid ester moiety.
WIN 55,212-2 is a potent cannabinoid receptor agonist.
IRI prefix change from BAO_02000 to BAO_00012 in January 2017
ethyleneglycol-bis(β-aminoethyl)-N,N,N′,N′-tetraacetic acid
The serum used in cell culture medium. Cultured cells require serum or growth factors for growth by cell division. In the laboratory, each cell type is grown in a medium supplemented with a variable concentration of serum (up to 20%) which is optimized for its growth. Specialized sera include dextran charcoal treated serum, which lacks certain hormones, growth factors, etc, dialyzed serum, which lacks low molecular weight molecules (below 10,000 MW), such as glucose, amino acids, low molecular weight hormones, cytokines, etc. Most commonly, fetal bovine serum is used in cell culture, but other sera such as horse serum are also used.
The serum used in assay medium while performing a cell-based assay and is optimized for each assay type. In certain assays, the cells could be maintained at either a lower concentration of the serum or in a specialized serum, including dextran charcoal treated serum, dialyzed serum, etc. This is done to avoid interference with the assay measurements.
phosphatidylinositol (3,4,5)-triphosphate
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity (from OBI).
piperazine-N,N'-bis(2-ethanesulfonic acid)
tris(2-carboxyethyl)phosphine hydrochloride
A fluorinated 4-methylumbelliferyl phosphate (MUP) derivative that has a lower pKa than that of MUP, making DiFMUP an excellent substrate for continuously assaying acid phosphatases at low pH. The reaction product of DiFMUP has excitation/emission maxima of ~358/450 nm.
6,8-Difluoro-4-Methylumbelliferyl Phosphate
alamarBlue is a cell viability assay reagent which contains the cell permeable, non-toxic, and weakly fluorescent blue indicator dye called resazurin.
Fluorescent dye with an excitation/emission maxima of ~555/580 nm.
Fluorescent dye with an excitation/emission maxima of ~578/603 nm.
Common buffer component with the chemical formula NH4CH3CO2.
Organic solvent which allows for the denaturation and renaturation of nucleic acids at room temperature. Often used as a quenching agent.
Hygroscopic salt commonly used in buffers