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41 protocols using sephacryl s 300

1

Purification of Hyperimmune Egg Yolk IgY

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The egg yolks from hyperimmunized hens were physically separated from the egg white and first mixed gently with eight volumes of cold distilled water (acidified with 0.1 M HCl to give pH 4.0) to avoid possible disruptions of egg yolk granules due to the presence of high concentrations of acid. Cold acidified distilled water (pH 2.0) was then added to make a final dilution of 1:10. After mixing well, the mixture was adjusted to a pH 5.0-5.2 and incubated at 4 °C for 12 h. The WSF was obtained by centrifugation at 3.125 x g at 4 °C for 20 min. The supernatant was collected as the IgY rich WSF and titrated by indirect ELISA (mentioned below) using Sigma gliadin as a coating antigen. The WSF (10 mg protein/ml) of high titre was further purified by using a 1.0 x 110 cm column of Sephacryl S-300 (GE Healthcare, Piscataway, NJ) which was equilibrated and eluted with PBS at a flow rate of 3 ml/h. Blue dextran (Pharmacia Biotech Inc., Baie-d’Urfe, QC) and titrated water were used to determine void volume (Vo) and total volume (Vt) of the column, respectively. The partition coefficient was calculated from the formula: Kav = (Ve - Vo)/(Vt - Vo), in which Ve represents the volume of the peak fraction. The eluates (1 ml) were analyzed for IgY activity at 405 nm by ELISA. The eluates of IgY were pooled, freeze-dried and analyzed for protein content, total IgY and specific IgY.
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2

Recombinant Histone Reconstitution and Purification

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Consensus sequences for human histones H2A, H2B and H3.2 and Xenopus histone H4 were cloned into pST50 expression vectors, expressed in BL21(DE3)pLysS Escherichia coli, purified from inclusion bodies and reconstituted into H2A–H2B dimers or H3–H4 tetramers exactly as previously described (58 (link)). Histone H3 was purified from inclusion bodies, solubilized in 7 M guanidine and purified by size exclusion chromatography (Sephacryl S300, GE Healthcare) followed by Source S cation exchange chromatography as previously reported (59 (link)). After purification, the histone was lyophilized and resuspended in water with 1 mM DTT. Plasmids containing repeats of widom 601 sequences (60 (link)) were gifts from Song Tan (61 (link)). Plasmids were amplified in HB101 E. coli and purified by alkaline lysis. Nucleosomal DNA fragments were excised from plasmid DNA using EcoRV and purified by anion exchange chromatography with a Source Q resin (GE Healthcare). Nucleosomes and tetrasomes were prepared by salt gradient dialysis as previously described (45 (link),58 (link),59 (link)). FLAG-tagged histone H2A–H2B dimers were prepared by coexpression and PEI precipitation followed by cation exchange chromatography using a Source S resin (GE Healthcare) as previously described (58 (link)).
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3

Recombinant LCN-2 Protein Expression

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Full length LCN-2 cDNA was synthesized by GeneScipt, USA. It was subcloned in pET28a vector at NdeI and XhoI restriction site. The construct was transformed into E.coli DH5-α cells for amplification and E.coli Rosetta for expression. A single colony was grown overnight as a mother culture. 10% of mother culture was inoculated and grown to 0.8–1.0 OD and induced with 0.5 mM IPTG for 2 h at 37 °C. The cells were then pelleted by centrifugation at 6000 rpm for 10 min at 4 °C in a microfuge, resuspended in 10% volume of 20 mM Tris pH 8.0, containing 300 mM NaCl and 10% Glycerol. The mixture was sonicated for 30 s on and off each for 6 cycles, and then centrifuged at 12000 rpm for 30 min at 4 °C. The supernatant fraction was passed over a Nickel NTA (BioVision, USA) column as per the manufacturer’s protocol. The column was washed twice with 10 times the bed volume with 20 mM Tris pH 8.0, with 300 mM NaCl, 10% Glycerol and 20 mM Imidazole. The protein was eluted with 20 mM Tris pH 8.0, 300 mM NaCl, 10% Glycerol and 300 mM Imidazole with approximately five times the bed volume in multiple fractions. The protein was polished over Sephacryl S-300 (GE Healthcare, USA, GE17–0599–10) following overnight dialysis at 4 °C in 1X PBS and 50% Glycerol. The filter (0.25 micron) sterilized protein was stored at −20 °C in working aliquots.
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4

Synthesis and Characterization of Photopolymer Hydrogels

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Citric acid (99.5–100%) was purchased from VWR (West Chester, PA, USA). 1,2-phenylenediamine flakes (99.5%) and cross-linked sodium polyacrylate (SPA) were obtained from Sigma-Aldrich (St. Louis, MO, USA). The commercial FLGPCL02 photopolymer was bought from formlabs (Somerville, MA, USA) with a viscosity of between 850 and 900 cps and a data sheet containing its physical properties in the supporting information. The Orbeez commercial SPA-based beads were provided by Toys“R”Us (Miami, FL, USA) with a data sheet in the supporting information. The distilled water used was purified using a Modulab 2020 water purification system acquired from Continental Water System Corporation (San Antonio, TX, USA). The water had a pH of 6.62 ± 0.3 at 25 ± 0.5 °C. The SEC was performed using GE Healthcare Sephacryl S-300 (Uppsala, Sweden) as the matrix. All the chemicals were used without further treatment.
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5

Recombinant hnRNP A2 Purification

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Expression and purification of recombinant hnRNP A2 was performed as described (Munro et al., 1999 (link); Muslimov et al., 2011 (link)). Escherichia coli BL21(DE3) was transformed with plasmid pET-9c/A2 to express hnRNP A2. Cells were induced with isopropyl-β-d-thiogalactopyranoside. Harvested by centrifugation, cells were lysed in 50 mM Tris-HCl, pH 8, 2 mM EDTA, 100 µg/ml lysozyme, and 0.1% Triton X-100. Buffer A (50 mM Tris-HCl, pH 8.5, 0.2 mM EDTA, and 5% wt/vol glycerol) was used for dialysis of the soluble fraction. Chromatography was performed on diethylaminoethyl cellulose (GE Healthcare) and, subsequently, on Sephacryl S-300 (GE Healthcare) and, for further purification, on a C4 reverse-phase HPLC column (Vydac) using a linear 10–50% acetonitrile gradient in 0.1% trifluoroacetic acid. After lyophilization, hnRNP A2 was dissolved in water. Protein identity and purity was ascertained by SDS-PAGE and by electrospray mass spectrometry on a spectrometer (Sciex 165; PerkinElmer).
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6

Allyl Dextran-Based Size-Exclusion Chromatography

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Allyl dextran-based size-exclusion gel (Sephacryl S-300, GE Healthcare) was used as stationary phase. The gel column was prepared by filling a 15 cm long column with an appropriate amount of allyl dextran-based size-exclusion gel dilute 1:1 with the following solution buffer: 10 mM KCl, 20 mM TEA-HCl (pH 7.5), and 20 mM MgCl2. The flow rate of the running buffer was 1 ml/min and the presence of molecules along the flow was monitored by reading the absorbance at 254 nm with the EM-1 Econo UV absorbance instrument (Bio-Rad). The speed of the recording pare was set to 1 cm/min.
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7

Molecular Mass Determination of F. plautii DAEase

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The subunit molecular mass of F. plautiiDAEase was determined by SDS-PAGE under denaturing conditions, using a ladder of pre-stained proteins (MBI fermentas, Hanover, MD, USA) as references. All protein bands were stained with Coomassie Blue for visualization. The molecular mass of the native enzyme was investigated by gel-filtration chromatography using a Sephacryl S-300 preparative-grade column HR 16/60 (GE Healthcare, Piscataway, NJ, USA). The purified enzyme was loaded onto the column and eluted with 50 mM Tris-HCl (pH 7.5) buffer containing 150 mM NaCl at a flow rate of 1mL/min. The column was calibrated with ferritin (440 kDa), catalase (206 kDa), aldolase (158 kDa), and conalbumin (75 kDa) as reference proteins (GE Healthcare). The molecular mass of the native enzyme was calculated by comparing with the migration length with that of the reference proteins.
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8

Cryo-EM Structure of RUVBL1-RUVBL2 Complex

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For cryo-EM, we produced the human RUVBL1-RUVBL2 protein complex, as described previously (17 (link), 21 (link)). Affinity purification using a nickel column (His-tag purification) was followed by Sephacryl S300 (GE Healthcare) size-exclusion chromatography in a buffer containing 50 mM tris, 300 mM NaCl, and 1 mM dithiothreitol. The purified RUVBL1-RUVBL2 complexes used for cryo-EM contain a His-tag at the N terminus of RUVBL1, but the RUVBL2 subunit, with which PIH1D1 interacts, does not have a tag. For pull-down experiments, we cloned a RUVBL1-RUVBL2 complex without tag in RUVBL1 and a C-terminal strep-tag in RUVBL2 and purified it by affinity purification, followed by gel filtration.
We purified the RPAP3400–665-PIH1D1 complex, as described previously (17 (link)). Briefly, we used glutathione S-transferase (GST)–tag affinity chromatography to bind GST-RPAP3400–665, and we eluted the protein using 50 mM glutathione. We incubated the elution with PreScission protease (3C protease) at 4°C overnight to remove the tag, followed by a subsequent gel filtration chromatography using an S200 26/60 column. We reconstituted R2TP-ΔNT by mixing RUVBL1-RUVBL2 and RPAP3400–665-PIH1D1 subcomplexes in a 1:4 molar ratio, followed by dialysis in 25 mM Hepes (pH 7.8), 130 mM NaCl, and 10 mM 2-mercaptoethanol–containing buffer containing 0.5 mM ADP (pH 7.0) at 4°C for 4 hours.
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9

Tetanus Toxoid Purification Protocol

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CRM197, DT and TT were obtained from GSK Vaccines S.r.l., Siena. Tetanus toxoid was purified by gel filtration through Sephacryl S300 (GE Healthcare) equilibrated in 0.15 M NaCl, 10 mM NaH2PO4, pH 7.2. The fractions corresponding to the monomeric MW of TT were pooled and used for conjugation.
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10

Cinnamic Acid Derivatives Extraction

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Five cinnamic acid derivatives used in this study were purchased from J&K Chemical (Beijing, China). Ferrous ion chelator 3-(2-pyridyl)-5,6-bis(4-phenylsulfonic acid)-1,2,4-triazine (ferrozine) was obtained from Sigma-Aldrich Chemical Co. (Beijing, China). Sephacryl S-300, DEAE Sepharose Fast Flow, native electrophoresis marker, and SDS electrophoresis marker were purchased from GE Healthcare Bio-Sciences AB (Beijing, China). Sodium citrate, terephthalic acid (TA) and magnesium chloride hexahydrate were obtained from Beijing Chemical Reagents Co. (Beijing, China). All other reagents used were of analytical grade or purer.
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