4-(4-dimethylaminophenylazo)benzoic acid
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Most cited protocols related to «4-(4-dimethylaminophenylazo)benzoic acid»
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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-
(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.
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.
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.
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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To calculate the dimer dissociation constant (Kd), the velocities of enzyme titration of WT and mutant 3CLpros were fitted to
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.
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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More about "4-(4-dimethylaminophenylazo)benzoic acid"
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.
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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.
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