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10 protocols using lemo21 de3 cells

1

Mutagenesis Protocol for Protein Expression

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All primers for mutagenesis were ordered from Integrated DNA Technologies (IDT). Mutagenic primers were designed to anneal >18bp on either side of the site for mutagenesis with the desired mutation encoded in the primer. PCR was used to create fragments upstream and downstream of the mutation site with >20bp overlap with the desired pET vector. The resulting amplicons were isothermally assembled into either pET21b, pET28b, or pET29b restriction digested with XhoI and NdeI and transformed into chemically competent E. coli XL1-Blue cells. Monoclonal colonies were sequenced with Sanger sequencing. Sequence verified plasmid was purified using Qiagen miniprep kit and transformed into chemically competent E. coli BL21(DE3)Star, BL21(DE3)Star-pLysS cells (Invitrogen), or Lemo21(DE3) cells (NEB) for protein expression.
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2

High-Throughput Bacterial Protein Expression

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Plasmids were transformed into Lemo21(DE3) cells (New England Biolabs), and grown in 96 deepwell plates overnight at 37 °C in 1 mL of LB containing 50 ug/mL of kanamycin sulfate. The next day, 100 uL of overnight cultures were used to inoculate 96 deepwell plates containing 900 uL of TBII medium (MP Biomedicals) with 50 ug/mL of kanamycin sulfate, and the cultures were grown for 2 h at 37 °C before induction with 0.1 mM IPTG. Protein expression was carried out at 37 °C for 4 h before the cells were harvested by centrifugation (4,000 x g, 5 min). Cell pellets were resuspended in 100 uL of lysis buffer (10 mM sodium phosphate, 150 mM NaCl, pH 7.4, 1 mg/mL lysozyme, 0.1 mg/mL DNAse I, 5 mM MgCl2, 1 tablet/50 mL of cOmplete protease inhibitor (Roche), 0.05% v/v Tween 20), and cell were lysed by performing three freeze/thaw cycles (1 h incubations at 37 °C followed by freezing at −80 °C). The lysate was cleared by centrifugation (4,000 x g, 20 min), and the soluble fraction transferred to a 96 well assay plate (Corning, cat #3991). Concentrations of the constructs in soluble lysate were determined by sfGFP fluorescence using a calibration curve.
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3

Heterologous Protein Expression in E. coli

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Synthetic genes were ordered from Genscript Inc. (Piscataway, NJ, USA) and delivered in pET 28b+, pET21b+, or pET29b+ E. coli expression vectors, inserted at the NdeI and XhoI sites of each vector. For pET28b+ constructs, synthesized DNA was cloned in frame with the N-terminal hexahistidine tag and thrombin cleavage site and a stop codon was added at the C-terminus. For pET21b+ constructs, a stop codon was added at the C-terminus such that the protein was expressed with no hexahistidine tag. For pET29b+ constructs, the synthesized DNA was cloned in frame with the C-terminal hexahistidine tag. Plasmids were transformed into chemically competent E. coli BL21(DE3)Star, BL21(DE3)Star-pLysS cells (Invitrogen), or Lemo21(DE3) cells (NEB) for protein expression.
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4

Heterologous Protein Expression in E. coli

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Synthetic genes were ordered from Genscript Inc. (Piscataway, NJ, USA) and delivered in pET 28b+, pET21b+, or pET29b+ E. coli expression vectors, inserted at the NdeI and XhoI sites of each vector. For pET28b+ constructs, synthesized DNA was cloned in frame with the N-terminal hexahistidine tag and thrombin cleavage site and a stop codon was added at the C-terminus. For pET21b+ constructs, a stop codon was added at the C-terminus such that the protein was expressed with no hexahistidine tag. For pET29b+ constructs, the synthesized DNA was cloned in frame with the C-terminal hexahistidine tag. Plasmids were transformed into chemically competent E. coli BL21(DE3)Star, BL21(DE3)Star-pLysS cells (Invitrogen), or Lemo21(DE3) cells (NEB) for protein expression.
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5

Mutagenesis Protocol for Protein Expression

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All primers for mutagenesis were ordered from Integrated DNA Technologies (IDT). Mutagenic primers were designed to anneal >18bp on either side of the site for mutagenesis with the desired mutation encoded in the primer. PCR was used to create fragments upstream and downstream of the mutation site with >20bp overlap with the desired pET vector. The resulting amplicons were isothermally assembled into either pET21b, pET28b, or pET29b restriction digested with XhoI and NdeI and transformed into chemically competent E. coli XL1-Blue cells. Monoclonal colonies were sequenced with Sanger sequencing. Sequence verified plasmid was purified using Qiagen miniprep kit and transformed into chemically competent E. coli BL21(DE3)Star, BL21(DE3)Star-pLysS cells (Invitrogen), or Lemo21(DE3) cells (NEB) for protein expression.
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6

Optimized Expression of SmTetX Protein in E. coli

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The target amino-acid sequence (NCBI Reference Sequence WP_049406473) was back-translated and codon usage was optimized for expression in E. coli with OPTIMIZER (Puigbò et al., 2007 ▸ ). A plasmid encoding the SmTetX protein including a 6×His tag at the N-terminus of the translated protein was synthesized and cloned into the pET-28a(+)-TEV expression vector via NdeI and BamHI restriction sites by GenScript, USA. The cleavage site for Tobacco etch virus (TEV) protease was placed between the His tag and the target SmTetX sequence (Supplementary Fig. S1).
The plasmid was transformed into competent E. coli strain Lemo21 (DE3) cells (New England Biolabs) using the heat-shock method. Cell precultures in LB medium were incubated in a shaker at 32°C and 180 rev min−1 overnight. The medium was supplemented with 50 µg ml−1 kanamycin and 25 µg ml−1 chloramphenicol. 10 ml preculture was added to 1 l Power Broth medium (Molecular Dimensions, catalogue No. MD12-106) and the cell culture was incubated at 30°C and 150 rev min−1 until the OD600 reached ∼0.5. Expression was induced with 1 mM isopropyl β-d-1-thiogalactopyranoside (IPTG) at 20°C for 16 h. The cells were harvested after centrifugation of the culture at 4°C and 5000g for 30 min.
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7

Recombinant SARS-CoV-2 Nucleocapsid Protein Production

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The sequence of the SARS-CoV-2 nucleocapsid gene was obtained from GenBank (Accession number: MN988669.1). Codon was optimized for protein expression in E. coli and cloned in NheI and NotI sites of the pET-28a (+) plasmid by GenScript (USA) to produce the recombinant protein with an n-terminal 6x His tag. Lemo21 (DE3) cells (New England BioLabs, USA) were transformed with pET28a + N by electroporation. A positive clone was cultured overnight using a shaker at 37 °C, 200 rpm, in Lauria Bertani Broth (LB) liquid medium by selective pressure with kanamycin (50 μg/mL) and chloramphenicol (34 μg/mL). The overnight culture was inoculated in fresh medium containing both antibiotics and grown using a Biostat B benchtop bioreactor (Sartorius, Germany) at 37 °C, 500 rotations per minute (rpm) until the optical density at 600 nm reaches about 0.6. Then, expression was induced by the addition of IPTG to a final concentration of 0.4 mM. The temperature was reduced to 30 °C and expression was carried out for 3 h.
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8

Affinity Purification of Stim1 and Orai1

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The fragments of Stim1 (342–448, 344–382 and 408–442) and Orai1 (1–103, 1–47, 48–103, 228–301, 245–272 and 272–292) were amplified from full length constructs and cloned into pMAL-c5X (New England Biolabs) or pGEX-4T2 (Addgene) vector, in-frame with MBP or GST protein coding sequences, respectively. The fusion proteins were expressed in LEMO21(DE3) cells (New England Biolabs) by inducing with IPTG (0.3 mM) for 14 hours at 18°C. The MBP- or GST-tagged proteins were purified by immobilizing on amylose (NEB) or glutathione resin (Qiagen), respectively. The resin bound proteins were incubated with 20–50 nM of α-SNAP protein in Ringer’s buffer containing 0.1% NP-40 and 2 mM imidazole for 1 hr at 4°C. The resin was washed thrice with Ringer’s buffer, boiled in SDS sample buffer and subjected to SDS-PAGE followed by Western Blot analysis.
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9

Enzyme Purification and Storage Protocol

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Enzyme variants were expressed in Lemo21(DE3) cells (New England Biolabs, Ipswich, MA, USA), and purification done in one step on a StrepTactin column by a protocol that has been described elsewhere 19. The enzyme was eluted in 25 mm Tris, pH 8.0, 10 mm MgCl2, 2.5 mm desthiobiotin, with 15% v/v ethylene glycol added as a storage medium to prevent frost damage. Enzyme purity was judged to be 95–99% pure by SDS/PAGE on 4–12% bis‐Tris NUPAGE® gels (Life technologies, Carlsbad, CA, USA). Enzymes were snap‐frozen and stored at −20 °C and never used in analysis after more than one freeze/thaw cycle. For denaturation and refolding studies, the enzyme was concentrated on HiTrap Q XL (GE Healthcare, Chicago, IL, USA) ion exchange column on a low‐pressure Bio‐Rad BioLogic LP Chromatography System and eluted with a NaCl gradient from 0.0 to 1.0 m and then further concentrated on a 2.0‐mL Amicon Ultra centrifugation filter with a 30k cut‐off (Millipore, Burlington, MA, USA). Concentrated enzyme samples were aliquoted to 10 μL single use portions and stored at −20 °C.
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10

High-Throughput Bacterial Protein Expression

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Plasmids were transformed into Lemo21(DE3) cells (New England Biolabs), and grown in 96 deepwell plates overnight at 37 °C in 1 mL of LB containing 50 ug/mL of kanamycin sulfate. The next day, 100 uL of overnight cultures were used to inoculate 96 deepwell plates containing 900 uL of TBII medium (MP Biomedicals) with 50 ug/mL of kanamycin sulfate, and the cultures were grown for 2 h at 37 °C before induction with 0.1 mM IPTG. Protein expression was carried out at 37 °C for 4 h before the cells were harvested by centrifugation (4,000 x g, 5 min). Cell pellets were resuspended in 100 uL of lysis buffer (10 mM sodium phosphate, 150 mM NaCl, pH 7.4, 1 mg/mL lysozyme, 0.1 mg/mL DNAse I, 5 mM MgCl2, 1 tablet/50 mL of cOmplete protease inhibitor (Roche), 0.05% v/v Tween 20), and cell were lysed by performing three freeze/thaw cycles (1 h incubations at 37 °C followed by freezing at −80 °C). The lysate was cleared by centrifugation (4,000 x g, 20 min), and the soluble fraction transferred to a 96 well assay plate (Corning, cat #3991). Concentrations of the constructs in soluble lysate were determined by sfGFP fluorescence using a calibration curve.
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