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Dimethyl pimelimidate dihydrochloride dmp

Manufactured by Merck Group
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Dimethyl pimelimidate dihydrochloride (DMP) is a chemical crosslinking agent used in various laboratory applications. It is a water-soluble, amine-reactive compound that can form stable covalent bonds between primary amines. DMP is commonly used for the immobilization, stabilization, or conjugation of proteins, peptides, or other biomolecules in biochemical and analytical procedures.

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8 protocols using dimethyl pimelimidate dihydrochloride dmp

1

Antibody Immobilization on Protein A-Sepharose

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One milliliter Protein A-sepharose beads (GE Healthcare) were washed in 50 mM borate, 50 mM KCl (pH 8.0) solution, and then incubated with 2 mg of antibody slowly rotating 1 h in cold room. Beads were washed with 0.2 M triethanolamine (pH 8.2) and cross-linked with 40 mM dimethyl pimelimidate dihydrochloride (DMP) (Sigma) (pH 8.3) for 1 h at room temperature. Ice-cold 0.2 M Tris buffer (pH 8.0) was added to stop the reaction, and beads were washed with 0.1 M citrate (pH 3.0), and finally 50 mM Tris (pH 8.0).
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2

Synthesis and Characterization of Zinc Oxide Nanoparticles

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All experimental reagents were analytically pure and used without further purification. Zinc nitrate hexahydrate (ZnNO3•6H2O, 98%), ammonium hydroxide solution (28% NH3 in H2O, 99.99% trace metal reference), dimethyl pimelimidate dihydrochloride (DMP, Sigma, D8388-5G), dimethyl suberimidate dihydrochloride (DMS, Sigma, 179523-5G), hematoxylin and eosin stain (H&E, Sigma, CAS No.:517-28-2 and CAS No.:56360-46-4), and periodic acid−Schiff (PAS, Sigma, CAS No.:10450-60-9) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Sodium dodecyl sulfate (SDS, Sigma, CAS No.: 151-21-3) was bought from Welgene (Daegu, Korea). Cetyltrimethylammonium bromide (C19H42BrN, >98%, CTAB, Sigma, CAS No.: 57-09-0) was purchased from Tokyo Chemical Industry Co., Ltd. (Tokyo, Japan). Sabot’s dextrose agar and chloramphenicol medium containing chloramphenicol medium (Cat #C6781; Lot #437412) were purchased from Santa Maria. Milli-Q water and phosphate-buffered saline (PBS, 10X, pH 7.4, Thermo Fisher Scientific, CAS No.: 12579099) were used in all the experiments.
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3

Covalent Antibody Immobilization on Silicon

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The oxidized silicon surface of the chip was primed by incubating in 1 mM NHS-silane solution ((CH3)2SiCl(CH2)4COONHS, ProChimia Surfaces, Poland) for 2 hours at room temperature, resulting in the formation of a self-assembled monolayer exposing NHS-ester groups. The primary amine groups on protein molecules can readily replace the NHS ester groups, forming covalent protein immobilization on the surface. Then 100 μL of 1 mg/mL recombinant protein A/G (Pierce™, Thermo Fisher) was introduced to form an intermediate layer for grafting the Fc domains of antibodies. 100 μL of 3 mg/mL pan-HLA antibodies were subsequently introduced. To avoid a co-elution of antibodies in the final peptide sample, we crosslinked the antibodies on the protein A/G layer by 20 mM dimethyl pimelimidate dihydrochloride (DMP, Sigma-Aldrich) dissolved in 0.2 M sodium borate buffer (pH 9, Sigma-Aldrich). The reaction was quenched by 0.2 M ethanolamine (pH 8, Sigma-Aldrich). The crosslinked chips were stored in 0.02% sodium azide solution at 4°C until use.
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4

Receptor Binding and Interaction Assays

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IBOP ([1S-[1α,2α(Z),3β(1E,3S),4α]]-7-[3-[3-hydroxy-4-(4-iodophenoxy)-1-butenyl]-7-oxabicyclo[2.2.1]hept-2-yl]-5-heptenoic acid), SQ29548 ([(1S)1α,2β(5Z)3α,4β]-7-[3-[2-(phenylamino)carbonyl-hydrazino-methyl]-7-oxabicyclo-[2.2.1]-hept-2-yl]-5-heptenoic acid), and Gö6983 were obtained from Cayman Chemical Co. (Ann Arbor, MI, USA). AG1478 was from Calbiochem (San Diego, CA, USA). Bradykinin B-3259 (Arg-Pro-Pro-Gly-Phe-Ser-Pro-Phe-Arg), Dimethyl pimelimidate dihydrochloride (DMP), and Duolink detection kit were purchased from Sigma-Aldrich (St. Louis, MO, USA).
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5

Immunoaffinity Purification of Proteins

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Ten milliliters of hybridoma supernatant was added to 50 μl of slurry Protein G Sepharose beads and rotated at room temperature for 1 h. The Protein G Sepharose-antibody beads were washed with borate buffered saline (0.2 M boric acid/NaOH pH 9.0) three times and rotated with 5.2 mg/ml dimethyl-pimelimidate-dihydrochloride (DMP, Sigma-Aldrich) in Borate buffered saline for 30 min. The beads were then washed two times with 0.2 M ethanolamine, rotated for 2 h with 0.2 M ethanolamine (pH 8) and washed three times with PBS. Hemocytes were isolated from the hemolymph, by centrifugation (4°C, 1800 rpm, 8 min). The cells were extracted in lysis buffer containing 50 mM Tris/HCl (Reanal) pH 8.0, 150 mM MgCl 2 (Reanal), 1% NP40 (Fluka), 5 mM EDTA (Sigma), 0.1% SDS (Sigma), 10 mM PMSF (Sigma) and Complete Protease Inhibitor Cocktail (Roche), according to the manufacturer's instructions, for one hour. Fifty µl (20% Protein G Sepharose) beads were mixed with 300µl hemocyte lysate and incubated overnight at 4°C. Then the beads were washed three times with lysis buffer and incubated in SDS-PAGE sample buffer (15.6 mM Tris/HCl pH 6.8, 6.25% glycerol, 0.5% SDS, 0.003% bromophenol blue) for one hour at 56°C and subsequently boiled for 5 min. The resulting samples were analyzed with SDS-PAGE/Western blot.
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6

Isotopic Labeling and Immunoprecipitation Mass Spectrometry

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All reagents and solvents were liquid chromatography (LC)/mass spectrometry (MS)-grade quality unless otherwise noted. [13C6]-leucine was obtained from Cambridge Isotope Laboratories (Andover, MA). Anti-FXN recombinant rabbit monoclonal antibody (mAb) EPR21840 (cat. # ab219414) was from Abcam (Cambridge, UK). Ethylenediaminetetraacetic acid (EDTA)-free protease inhibitor cocktail, DL-dithiothreitol (DTT), EDTA-free Easypack protease inhibitor cocktail tablets, and dimethyl pimelimidate dihydrochloride (DMP) were purchased from MilliporeSigma (Billerica, MA). LC-grade water and acetonitrile were obtained from Burdick and Jackson (Muskegon, MI). Protein G Dynabeads for immunoprecipitation (IP) and radioimmunoprecipitation assay (RIPA) lysis buffer with EDTA were from ThermoFisher Scientific (Waltham, MA). LC/MS grade water and Optima LC/MS grade solvents were from Fisher Scientific (Pittsburgh, PA).
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7

Quantitative Proteomic Analysis of Frataxin

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All reagents and solvents were LC-MS grade quality unless otherwise noted. [13C615N2]-lysine and [13C615N1]-leucine were from Cambridge Isotope Laboratories (Andover, MA, United States). Anti-frataxin mouse monoclonal antibody [17A11] Ab113691 was from Abcam (Cambridge, MA, United States). Dimethyl pimelimidate dihydrochloride (DMP), Ethylenediaminetetraacetic acid (EDTA), cOmplete™ Mini EDTA-free Easypack protease inhibitor cocktail tablets, endoproteinase Asp-N sequencing grade, DL-dithiothreitol (DTT), bovine serum albumin (BSA), human lysozyme, imidazole, glycerol, phenylmethylsulfonyl fluoride (PMSF), triethanolamine, ethanolamine, and M9, minimal salts, 5X powder, minimal microbial growth medium (M9 media) were purchased from MilliporeSigma (Billerica, MA, United States). Ni-NTA agarose resin was purchased from Qiagen (Germantown, MD, United States). LC grade water and acetonitrile were from Burdick and Jackson (Muskegon, MI, United States). Ammonium bicarbonate and acetic acid were purchased from Fisher Scientific (Pittsburgh, PA, United States). Protein G magnetic beads were obtained from Life Technologies Corporation (Grand Island, NY, United States).
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8

Isotopic Labeling and Immunoprecipitation Mass Spectrometry

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All reagents and solvents were liquid chromatography (LC)/mass spectrometry (MS)-grade quality unless otherwise noted. [13C6]-leucine was obtained from Cambridge Isotope Laboratories (Andover, MA). Anti-FXN recombinant rabbit monoclonal antibody (mAb) EPR21840 (cat. # ab219414) was from Abcam (Cambridge, UK). Ethylenediaminetetraacetic acid (EDTA)-free protease inhibitor cocktail, DL-dithiothreitol (DTT), EDTA-free Easypack protease inhibitor cocktail tablets, and dimethyl pimelimidate dihydrochloride (DMP) were purchased from MilliporeSigma (Billerica, MA). LC-grade water and acetonitrile were obtained from Burdick and Jackson (Muskegon, MI). Protein G Dynabeads for immunoprecipitation (IP) and radioimmunoprecipitation assay (RIPA) lysis buffer with EDTA were from ThermoFisher Scientific (Waltham, MA). LC/MS grade water and Optima LC/MS grade solvents were from Fisher Scientific (Pittsburgh, PA).
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