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4-(4-dimethylaminophenylazo)benzoic acid

4-(4-Dimethylaminophenylazo)benzoic acid is a chemical compound used in various research applications.
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Most cited protocols related to «4-(4-dimethylaminophenylazo)benzoic acid»

Enzyme activity assays were performed using a fluorometric assay as previously described (9 (link)). Briefly, 10 μm of 3′ fluorescein-labeled oligonucleotides (GATCTGAGCCTGGGaGCT or gatctgagcctgggagct; uppercase DNA, lowercase RNA) were annealed to a complementary 5′ DABCYL-labeled DNA oligonucleotide (Eurogentec) in 60 mm KCl, 50 mm Tris-HCl, pH 8, by heating for 5 min at 95 °C followed by slow cooling to room temperature. Reactions were performed in 100 μl of buffer (60 mm KCl, 50 mm Tris-HCl, pH 8, 10 mm MgCl2, 0.01% BSA, 0.01% Triton X-100) with 250 nm substrate in 96-well flat-bottomed plates at 24 ± 2 °C for 90 min. Fluorescence was read for 100 ms using a VICTOR2 1420 multilabel counter (Perkin Elmer), with a 480 nm excitation filter and a 535 nm emission filter. Reactions were carried out in triplicate with a range of different protein concentrations. A standard curve (relating fluorescence units to moles of converted substrate) was generated using fluorescein-labeled oligonucleotide annealed to DNA without DABCYL.
Publication 2010
4-(4-dimethylaminophenylazo)benzoic acid Biological Assay Buffers DNA, Complementary Enzyme Assays Fluorescein Fluorescence Fluorometry Magnesium Chloride Nevus Oligonucleotides Staphylococcal Protein A Triton X-100 Tromethamine
The Km and Ki Assays were carried out as previously described40 (link), 41 (link). In the Km assay, a 10-amino acid substrate containing the natural MA/CA cut site with an EDANS/DABCYL FRET pair was dissolved in 8% DMSO at 40nM and 6% DMSO at 30 nM. The 30 nM of substrate was 4/5th serially diluted from 30 nM to 6 nM, including a 0 nM control. HIV protease was diluted to 120 nM and, using a PerkinElmer Envision plate reader, 5 μL was added to the 96-well plate to obtain a final concentration of 10 nM. The fluorescence was observed with an excitation at 340 nm and emission at 492 nm and monitored for 200 counts, for approximately 23 minutes. FRET inner filter effect correction was applied as previously described56 (link). Corrected data was analyzed with Prism7.
To determine the Ki, in a 96-well plate, each inhibitor was 2/3 serially diluted from 3000 pM to 52 pM, including a 0 pM control, and incubated with 0.35 nM protein for 1 hour. A 10-amino acid substrate containing an optimized protease cut site with an EDANS/DABCYL FRET pair was dissolved in 4% DMSO at 120 μM. Using the Envision plate reader, 5 μL of the 120 μM substrate was added to the 96-well plate to a final concentration of 10 μM. The fluorescence was observed with an excitation at 340 nm and emission at 492 nm and monitored for 200 counts, for approximately 60 minutes. Data was analyzed with Prism7.
Publication 2018
4-(4-dimethylaminophenylazo)benzoic acid 5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid Amino Acids Biological Assay Fluorescence HIV Protease Peptide Hydrolases Proteins Strains Sulfoxide, Dimethyl

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Publication 2012
4-(4-dimethylaminophenylazo)benzoic acid 5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid Biological Assay Cytokinesis Fluorescence Fluorescence Resonance Energy Transfer Fluorogenic Substrate Peptide Hydrolases Peptides Psychological Inhibition Severe acute respiratory syndrome-related coronavirus Tromethamine
3CLpro of SARS-CoV-2
with an N-terminal
MBP-tag, sensitive internally quenched fluorogenic substrate, and
assay buffer were obtained from BPS Bioscience (San Diego, CA, USA).
The enzyme was expressed in E. coli expression system,
and has a molecular weight of 77.5 kDa. The peptide substrate contains
a 14 amino sequence (KTSAVLQSGFRKME) with Dabcyl and Edans attached
on its N- and C-terminals, respectively. The reaction buffer is composed
of 20 mM Tris-HCl (pH 7.3), 100 mM NaCl, 1 mM EDTA, 0.01% BSA (bovine
serum albumin), and 1 mM 1,4-dithio-d,l-threitol
(DTT). GC376 (CAS No: 1416992-39-6) was purchased from Aobious (Gloucester,
MA, USA). Library of Pharmacologically Active Compounds (LOPAC) was
purchased from Sigma-Aldrich (St. Louis, MO, USA). All other compound
libraries were sourced by the National Center for Advancing Translational
Sciences (NCATS) including the NCATS Pharmaceutical Collection (NPC),29 (link) anti-infective, MIPE5.0, and NPACT libraries.
The LOPAC library has 1280 compounds consisting of marketed drugs
and pharmaceutically relevant structures with biological activities.
The NPC library contains 2552 FDA approved drugs, investigational
drugs, animal drugs, and anti-infectives. The anti-infective library
is a NCATS collection that contains 739 compounds that specifically
target viruses. The MIPE 5.0 library includes 2480 compounds that
are mixed with approved and investigational compounds, and mechanistic
based compounds focusing on oncology. The NPACT library contains 5099
structurally diverse compounds consisting of approved drugs, investigational
drugs, and natural products.
Publication 2020
4-(4-dimethylaminophenylazo)benzoic acid 5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid Albumins Animals Anti-Infective Agents Biopharmaceuticals Buffers cDNA Library Edetic Acid Enzymes Escherichia coli Fluorogenic Substrate GC376 Natural Products Neoplasms Peptides Pharmaceutical Preparations Severe acute respiratory syndrome-related coronavirus Sodium Chloride threitol Tromethamine Virus
Compounds in Table 1 were diluted in 25 mM Tris buffer (pH = 8.0) to a final concentration of 100 μM for screen. DMSO was used as a solvent control. In all, 10 μL compound solution was add to black 96-well plate (Greiner). In total, 30 μL of 2 μM GMpro was added to the plate and incubated with the compounds at 37 °C incubator for 30 min. In total, 330 μL of 25 mM Tris buffer was also added as blank control. Then 10 μL of 20 μM peptide substrate (Dabcyl-TSAVLQ↓SGFRKMK-Edans) solution (Genscript) in DMSO was added. The RFU value was measured with an excitation wavelength of 340 nm and emission wavelength of 490 nm at 37 °C for 1 h by using a microplate reader (TECAN Infinite 200 Pro, Switzerland). The RFU change curves vs time with or without inhibitors were plotted by GraphPad Prism 8.0.
Because GC376 and Boceprevir are time-dependent covalent inhibitors, we evaluated the enzyme inhibitory activity without any preincubation. In all, 20 mM GC376 and Boceprevir in DMSO were diluted to 60 μM to 0.015 μM and 120 μM to 0.03 μM by 25 mM Tris buffer (pH = 8.0) respectively. In total, 30 μL inhibitor solution with a series of concentration in 25 mM Tris buffer (pH = 8.0) was mixed with 10 μL of 100 μM peptide substrate firstly. In total, 30 μL Tris buffer was also mixed with 10 μL of 100 μM peptide substrate as negative control. Then, 10 μL of 200 nM final concentration of Mpro was added to the plate. The RFU value was measured with an excitation wavelength of 360 nm and emission wavelength of 490 nm at 37 °C for 1 h by using SpectraMax Paradigm Muti-Mode Detection Platform (Molecular Devices, USA)39 (link). Experiments were performed in triplicate. First 1200 s change of fluorescence value was used to calculate the reaction rate v0 by SoftMax Pro 7.1. The reaction rate of different inhibitor concentration is divided by the reaction rate of the negative control to calculate the inhibition rate with Microsoft Excel 2016. Inhibition curve was plotted by GraphPad Prism 8.0.
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Publication 2020
4-(4-dimethylaminophenylazo)benzoic acid 5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid boceprevir enzyme activity Fluorescence GC376 inhibitors Medical Devices Peptides prisma Psychological Inhibition Solvents Sulfoxide, Dimethyl Tromethamine

Most recents protocols related to «4-(4-dimethylaminophenylazo)benzoic acid»

Example 47

Azide Polymer Synthesis for Click Conjugation to Alkyne Terminated DNA Oligo

A solution of azidohexanoic acid NHS ester (2.5 mg) in anhydrous DMF (100 μL) was added to a solution of the amine-functional polymer (9.9 mg) in anhydrous DMF (100 μL) under argon. Diisopropylethylamine (2 μL) was then added. The reaction was agitated at room temperature for 15 hours. Water was then added (0.8 mL) and the azide-modified polymer was purified over a NAP-10 column. The eluent was freeze dried overnight. Yield 9.4 mg, 95%.

Oligo Synthesis with Pendant Alkyne (Hexyne) for Click Conjugation to Azide Polymer

The 3′ propanol oligo A8885 (sequence YATTTTACCCTCTGAAGGCTCCP, where Y=hexynyl group and P=propanol group) was synthesized using 3′ spacer SynBase™ CPG 1000 column on an Applied Biosystems 394 automated DNA/RNA synthesizer. A standard 1.0 mole phosphoramidite cycle of acid-catalyzed detritylation, coupling, capping and iodine oxidation was used. The coupling time for the standards monomers was 40 s, and the coupling time for the 5′ alkyne monomer was 10 min.

The oligo was cleaved from the solid support and deprotected by exposure to concentrated aqueous ammonia for 60 min at room temperature, followed by heating in a sealed tube for 5 h at 55° C. The oligo was then purified by RP-HPLC under standard conditions. Yield 34 OD.

Solution Phase Click Conjugation: Probe Synthesis

A solution of degassed copper sulphate pentahydrate (0.063 mg) in aqueous sodium chloride (0.2 M, 2.5 μL) was added to a degassed solution of tris-benzo triazole ligand (0.5 mg) and sodium ascorbate (0.5 mg) in aqueous sodium chloride (0.2 M, 12.5 μL). Subsequently, a degassed solution of oligo A8885 (50 nmole) in aqueous sodium chloride (0.2 M, 30 μL) and a degassed solution of azide polymer (4.5 mg) in anhydrous DMF (50 μL) were added, respectively. The reaction was degassed once more with argon for 30 s prior to sealing the tube and incubating at 55° C. for 2 h. Water (0.9 mL) was then added and the modified oligo was purified over a NAP-10 column. The eluent was freeze-dried overnight. The conjugate was isolated as a distinct band using PAGE purification and characterized by mass spectrometry. Yield estimated at 10-20%.

Fluorescence Studies

The oligo-polymer conjugate was used as a probe in fluorescence studies. The probe was hybridized with the target A8090 (sequence GGAGCCTTCAGAGGGTAAAAT-Dabcyl), which was labeled with dabcyl at the 3′ end to act as a fluorescence quencher. The target and probe were hybridized, and fluorescence monitored in a Peltier-controlled variable temperature fluorimeter. The fluorescence was scanned every 5° C. over a temperature range of 30° C. to 80° C. at a rate of 2° C./min. FIG. 25 shows increasing fluorescence intensity or emission with increasing temperature, indicating that as the probe-target pair melt, the polymer and quencher separate and fluorescence is recovered.

Polymer conjugation to nucleic acids can also be performed using methods adapted from the protocols described in Examples 14, 45 and 46.

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Patent 2024
4-(4-dimethylaminophenylazo)benzoic acid Acids Alkynes Amines Ammonia Anabolism Argon Azides DNA Replication Esters Fluorescence Freezing High-Performance Liquid Chromatographies Iodine Ligands Mass Spectrometry Moles Nucleic Acids Oligonucleotides phosphoramidite Polymers Propanols Sodium Ascorbate Sodium Chloride Spacer DNA Sulfate, Copper Triazoles Tromethamine

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Publication 2023
4-(4-dimethylaminophenylazo)benzoic acid 5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid Biological Assay Buffers Fluorescence Peptide Hydrolases Peptides prisma Psychological Inhibition SARS-CoV-2
The FRET-based assay was performed similarly to the self-assembled monolayers for matrix-assisted desorption/ionization mass spectrometry (SAMDI-MS) assay. Assays were performed in 20-μL volume in 384-well nonbinding low-volume plates (Greiner Bio-One, Monroe, NC) at ambient temperature. 3CLpro and its mutants were preincubated with inhibitors for 30 min. Reactions were initiated by the addition of a FRET-compatible peptide substrate, dabcyl-KTSAVLQSGFRKM-E(Edans)-NH2. Fluorescence was measured for 90 min at 2-min intervals using 340/460-excitation/emission filters on an Envision plate reader (Perkin Elmer). The IC50 values were calculated by fitting the curves using a four-parameter equation in GraphPad Prism.
To calculate the dimer dissociation constant (Kd), the velocities of enzyme titration of WT and mutant 3CLpros were fitted to equations 1 and 2.
V0=Vmax[S]/(Km+[S])
Vmax=Kcat[D]=KcatKd+4CTKd2+8KdCT8
Equation 2 was described previously for the calculation of the monomer dimer equilibrium dissociation constant (Kd) (28 (link)).
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Publication 2023
4-(4-dimethylaminophenylazo)benzoic acid 5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid Biological Assay Enzymes Fluorescence Fluorescence Resonance Energy Transfer inhibitors Mass Spectrometry Peptides prisma Titrimetry
ALG-097161, nirmatrelvir, and PF-00835231 were synthesized by Aligos Therapeutics and purified to >95% purity. The synthesis of ALG-097161 is described in Text S1. GS-441524 was obtained from MedChem Express (catalog [cat.] no. HY-103586). The African green monkey kidney VeroE6 cell line was purchased from ATCC (cat. no. CRL-1586) and maintained in Dulbecco’s modified Eagle’s medium (DMEM; Gibco cat. no. 41965-039) supplemented with 10% (vol/vol) heat-inactivated fetal calf serum (FCS).
The SARS-CoV-2 GHB-03021 (EPI ISL407976|2020-02-03) isolate was obtained from a Belgian patient returning from Wuhan in February 2020. The isolate was passaged 7 times on VeroE6 cells, which introduced two series of amino acid deletions in the spike protein (37 (link)).
SARS-CoV-2 3CLpro wild-type and mutant enzymes were produced as previously described (38 (link)). Peptide substrate (Dabcyl-KTSAVLQSGFRKM-E(Edans)-NH2) for FRET was sourced from Biopeptide (San Diego, CA) at >95% purity.
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Publication 2023
4-(4-dimethylaminophenylazo)benzoic acid 5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid Amino Acids Anabolism Cell Lines Cells Cercopithecus aethiops Eagle Enzymes Fetal Bovine Serum Fluorescence Resonance Energy Transfer Gene Deletion GS-441524 Kidney M protein, multiple myeloma nirmatrelvir Patients Peptides PF-00835231 SARS-CoV-2 Therapeutics
A slightly modified
protocol from the commercially available assay (BPS Bioscience) was
used. Dithiothreitol was substituted with tris(2-carboxyethyl)phosphine
(TCEP), the latter of which was found not to alter the activity of
the enzyme in the assay. The 3CLpro protease was thawed
on ice and activated by dilution to 10.0 ng/μL with assay buffer.
The enzyme solution was further diluted with assay buffer to 0.5 ng/μL.
Twenty microliters of the enzyme solution was mixed with 5 μL
of increasing concentrations of the complex [2% (v/v) DMSO] diluted
in assay buffer in the dark. The mixture was incubated for 30 min
at 37 °C with slow shaking. The substrate [Dabcyl-KTSAVLQSGFRKM-E(Edans)-NH2] was diluted to 50 μM, and 25 μL was added to
the enzyme mixture. The mixture was incubated for 4 h at 37 °C
with slow shaking. The generated fluorescence signal (λex = 360 nm; λem = 460 nm) was recorded with
a Synergy H4 (BioTek) microplate reader. As a positive control, the
known inhibitor GC376 (IC50 = 140 ± 20 nM) was used.
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Publication 2023
4-(4-dimethylaminophenylazo)benzoic acid 5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid Biological Assay Buffers Dithiothreitol Enzyme Assays Enzymes Fluorescence GC376 Intestinal Atresia, Multiple Peptide Hydrolases phosphine Sulfoxide, Dimethyl Technique, Dilution tris(2-carboxyethyl)phosphine Tromethamine

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Dabcyl-QALPETGEE-Edans is a fluorogenic peptide substrate used for the detection and measurement of protease activity. It consists of a fluorescent donor (Edans) and a quencher (Dabcyl) separated by a specific peptide sequence (QALPETGEE). The cleavage of the peptide bond by a protease separates the donor and quencher, resulting in an increase in fluorescence intensity that can be monitored.
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More about "4-(4-dimethylaminophenylazo)benzoic acid"

4-(4-Dimethylaminophenylazo)benzoic acid, also known as DMPABA or Disperse Yellow 7, is a chemical compound that has been widely used in various research applications.
This azo dye is particularly useful in spectrophotometric and fluorometric analyses, as well as in cell biology and biochemistry studies.
One of the key applications of DMPABA is as a fluorescent probe or quencher.
It can be used in conjunction with fluorescent labeling techniques, such as Dabcyl-QALPETGEE-Edans, to study protein-protein interactions, enzyme activities, and other biomolecular processes.
Researchers can leverage the optical properties of DMPABA to develop sensitive and efficient assays using instruments like the Envision plate reader, FLx800 microplate reader, and FluoDia T70 microplate reader.
In addition to fluorescence-based applications, DMPABA has been employed in colorimetric and absorbance-based analyses.
The compound's distinctive yellow color and strong absorbance properties make it useful for developing spectrophotometric methods, which can be analyzed using tools like the Prism 8 and Victor3 platforms.
These techniques are often used to quantify analytes, monitor chemical reactions, and study the kinetics of various biological systems.
DMPABA's solubility in organic solvents, such as DMSO, also allows it to be incorporated into cell-based assays and other in vitro experiments.
Researchers can leverage the compound's ability to interact with biomolecules and cellular components to investigate a wide range of biological processes, from signaling pathways to drug-target interactions.
To streamline the research process and optimize the use of DMPABA, researchers can utilize AI-driven comparison tools like PubCompare.ai.
This platform helps researchers quickly locate and compare protocols from literature, preprints, and patents, allowing them to identify the best approach for their specific project.
By leveraging the power of artificial intelligence, researchers can save time and enhance the efficiency of their DMPABA-related studies, ultimately accelerating scientific discoveries and advancements.
Whether you're studying the spectroscopic properties of DMPABA, developing novel fluorescence-based assays, or investigating its interactions with biological systems, the insights and tools discussed here can help you navigate your research more effectively.
With the right strategies and resources, you can maximize the potential of this versatile chemical compound and drive your projects forward with greater speed and precision.