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5 protocols using t7 express competent e coli cells

1

Cloning and Screening of MAO-N Variants

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Synthesised genes were ligated into a linearised pET16b expression vector (Novagen) using the In-Fusion cloning kit (Clontech), following the manufacturers' protocol. Plasmids were then transformed into T7 express competent E. coli cells (New England Biolabs) and spread onto LB agar plates (100 μg ml−1 ampicillin) and incubated overnight at 37°C. For direct functional screening, cells were spread onto a Hybond-N transfer membrane, which enabled the E. coli transformants to be transferred to an agar plate containing 1 mM isopropyl-beta-d-thiogalactopyranoside to induce protein expression. For MAO-N activity assays, the induced bacterial colonies were analysed for oxidase activity through the production of hydrogen peroxide by the colorimetric assay outlined by Alexeeva et al. (2002 (link), 2003 (link)) using α-methylbenzylamine as the substrate.
To determine the DNA sequence of the synthesised constructs, bacterial colonies were inoculated and grown in liquid culture (LB with 100 μg ml−1 ampicillin), followed by plasmid extraction (Spin Miniprep kit, Qiagen) and Sanger sequencing (DNA Sequencing Facility, University of Manchester).
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2

Cultivation of Rhodobacter capsulatus Strains

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Three Rhodobacter capsulatus strains were used in this study: rifampicin sensitive wild-type strain B10 (Wall et al., 1975 (link)), a rifampicin resistant derivative SB1003 (ATCC BAA-309) and an RcGTA overproducer strain DE442 (Ding et al., 2014 ; Fogg et al., 2012 (link)). All R. capsulatus cultures were grown at 30°C either aerated in the dark or in anoxic sealed tubes under constant illumination. Two growth media were used – YPS complex broth (0.3% w/v yeast extract, 0.3% w/v peptone, 2 mM MgCl2, 2 mM CaCl2) or RCV defined broth (10 mM potassium phosphate buffer, 0.4% w/v L-malic acid, 0.1% w/v (NH4)2SO4, 0.020% w/v MgSO4.7H2O, 0.0075% w/v CaCl2.2H2O, 0.0012% w/v FeSO4.7H2O, 0.0020% w/v Na2EDTA, 0.0001% w/v thiamine hydrochloride. Plus 1 mL of trace element solution - 0.07% w/v H3BO3, 0.040% w/v MnSO4.H2O, 0.019% w/v Na2MoO4.2H2O, 0.006% w/v ZnSO4.7H2O, 0.001% w/v Cu(NO3).3H2O. The pH was adjusted to 6.8 with NaOH). For agar plates, 1.5% w/v agar was added to the above broth recipes. The E. coli S17-1 strain (DSM 9079), which contains chromosomally integrated tra genes, was used as a donor for all conjugations. NEB 10-beta Competent E. coli cells (New England Biolabs) were used for standard cloning and plasmid maintenance; T7 Express Competent E. coli cells (New England Biolabs) were used for overexpression of proteins for purification.
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3

Cloning and Expressing Glycoside Hydrolases

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The 57 glycoside hydrolase enzymes found in the genome sequence of LL1355 were annotated with putative enzymatic activities based on their top hits by BLAST (NCBI-NIH). 27 different enzymes were selected from LL1355 and cloned into E. coli using the pEXP-5-NT/TOPO (Thermo Fisher Scientific) plasmid. The plasmids were then transformed into T7-Express competent E. coli cells (New England Biolabs, Ipswich, MA) to obtain strains which were subsequently used for protein expression. An empty pEXP-5-NT plasmid was also cloned to serve as a negative control.
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4

Expression and Purification of AlkB Enzymes

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AlkB enzymes (wild type, D135S and S135T) were expressed in T7 express competent E. coli cells (New England Biolabs Inc.). Cells were grown in a 2 l scale LB medium at 37°C until the OD600 reached 0.4–0.8. Isopropyl β-d-1-thiogalactopyranoside (IPTG) and freshly made FeSO4 solution were added to the culture to 1 mM and 5 μM, respectively, and the culture was grown at 30°C for additional 4 h to induce the AlkB expression. Cells were pelleted and resuspended in lysis buffer containing 10 mM Tris–HCl pH 7.4, 300 mM NaCl, 5% glycerol, 2 mM CaCl2, 10 mM MgCl2, 2 mM 2-mercaptoethanol and 1× protease inhibitor (Thermo Fisher Scientific). Cells were then lysed with sonication and centrifuged at 13 000 rpm for 45 min. The supernatant was first purified with a manual Ni-NTA column and eluted with a buffer containing 10 mM Tris–HCl pH 7.4, 300 mM NaCl and 250 mM imidazole. The protein was then further purified using Mono S chromatography. The protein was eluted with gradient buffers composed of different ratios of buffer A (10 mM Tris–HCl pH 7.4 and 100 mM NaCl) and buffer B (10 mM Tris–HCl pH 7.4 and 1.5 M NaCl) and then buffer exchanged to the storage buffer (10 mM Tris–HCl pH 7.4, 250 mM NaCl). Glycerol was then added to 30%. The protein was aliquoted, snap frozen in liquid nitrogen and stored at –80°C.
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5

Cloning and Co-expression of HpaII Methyltransferases

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Haemophilus influenzae was acquired from the American Type Culture Collection (ATCC® 49699™), and cultured in ATCC® Medium 814: GC Agar/Broth Medium (Teknova) at 37°C overnight with shaking. Total genomic DNA was isolated with the DNeasy Blood and Tissue Kit (Qiagen). The HpaII gene was amplified using forward primer GAGATATACCATGGCTGAATTTTTTTCTGGTAATAGAGG and reverse primer TCGAGGCTGCAGTTATAAGAATCTAATTTGTACGTTTAACTTAATAAAAAAATC (IDT, San Diego, CA) and the M. HpaII gene was amplified using forward primer AGATATACATATGAAAGATGTG TTAGATGATAA CTTGTTAG and reverse primer TCGAGGGTACCTCAGTCATATAAATTTCCTAATTTTTCT AAAATTTTCTTACCT (IDT, San Diego, CA). PCR was performed with Taq polymerase (Clontech) using the following cycle 95°C for 5 minutes, 40 cycles of (94°C for 15 seconds, 55°C for 15 seconds, 72°C for 1 minute), and 72°C for 5 minutes. The ~1100 bp HpaII PCR fragment was cloned using NcoI and PstI restriction sites in frame with the 5’ His tag of pETDuet-1 (EMD Millipore). The ~1100 bp M. HpaII PCR fragment was cloned using NdeI and KpnI into pACYCDuet-1 (EMD Millipore).
Recombinant vectors were isolated in 10-beta Competent E. coli cells (New England Biolabs). Co-transformations with pETDuet-1/HpaII and pACYCDuet-1/M. HpaII were executed in T7 Express Competent E. coli cells (New England Biolabs) by heat shock.
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