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7 protocols using e coli xl10 gold cells

1

Purification of Epitope-Tagged Human Topoisomerase I

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Anti-FLAG M2 monoclonal affinity gel, FLAG peptide, anti-FLAG M2 monoclonal antibody were purchased from Sigma-Aldrich and the antibody against the C-terminus of hTop1 from Abcam.
Saccharomyces cerevisiae Top1 null strain EKY3 (ura3-52, his3Δ200, leu2Δ1, trp1Δ63, top1::TRP1, MATα) was used to express the hTop1 gene. YCpGAL1-e-hTop1 single copy plasmid was previously described [20 (link)].
The 8bmut and the 8hmut mutants were generated using a site-directed-mutagenesis kit (Agilent Technologies) of the YCpGAL1-hTop1 in which the hTop1 is expressed under the galactose inducible promoter in a single-copy plasmid. The epitope-tagged construct YCpGAL1-e-hTop1 contains the N-terminal sequence FLAG: DYKDDDDY (indicated with ‘e’), recognized by the M2 monoclonal antibody. The epitope-tag was subcloned into YCpGAL1-hTop18bmut or YCpGAL1-hTop18hmut to produce the YCpGAL1-e-hTop18bmut and YCpGAL1-e-hTop18hmut. The plasmids were transformed into XL10-Gold E. coli cells (Agilent Technologies) and, then, extracted using Quiagen miniprep kit. Positive clones were identified by sequencing the hTop1 gene of the extracted plasmids. After the transformation in EKY3 yeast strain, the purification of hTop1 proteins was carried out essentially as previously described [21 (link)].
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2

Bacterial and Yeast Cell Culture Protocol

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XL10-Gold E. coli cells (Agilent) and E. coli BL21-CodonPlus (DE3)-RIL cells (Agilent) were cultivated in luria broth (LB) or terrific broth (TB) medium (RPI). The Bg12 strain of P. pastoris (Biogrammatics) was cultured in buffered minimal glycerol (BMGY) or buffered minimal methanol (BMMY) media containing yeast nitrogen base (Sigma-Aldrich). All cell lines used in this study were authenticated by the suppliers and were chosen to remain consistent with previous studies.
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3

Plasmid Constructs for Insulin Receptor Studies

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Plasmids were maintained in E. coli XL10-Gold cells (Agilent Technologies, Stockport, UK; cat. no. 200314). Standard protocols for plasmid constructions were used (Ausubel et al., 2017 ). Plasmid pmaxGFP was obtained from Lonza Cologne AG (Cologne, Germany). Plasmid pEGFP-N2-hINSR encodes a fusion of the human insulin receptor to eGFP (Bass et al., 2000 (link)) and was obtained from Addgene (Cambridge, MA; Addgene ID 22286). Plasmid pcDNA5/FRT/TO-FV2E-INSRβ was generated by cloning the 1430-base-pair BsiWI-XmaI fragment of pCLFv2IRE (Cotugno et al., 2004 (link)) into BsiWI- and XmaI-digested pcDNA5/FRT/TO-FV2E-C’hIRE1α (D. Cox and M. Schröder, Durham University, Durham, UK, unpublished data). Plasmid pcDNA5/FRT/TO-MyrFV2E-INSRβ was generated by cloning the 501-base-pair EcoRI-XmaI fragment of pC4M-FV2E (Ariad Pharmaceuticals, Cambridge, MA) into HindIII- and XmaI-digested pcDNA5/FRT/TO-FV2E-INSRβ after blunting the EcoRI and HindIII sites with Klenow enzyme.
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4

Genetic Engineering Techniques in E. coli

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Escherichia coli B40 (sup+), BL21 (DE3) (Tyr sup+), BL21 (DE3) (Gly sup+), and BL21 (DE3) (Arg sup+) were used as amber suppressors for initial crosses and preparation of phage stocks. The sup-E. coli P301 (B strain) and sup-E. coli D21 (K12 strain) (E. coli Genomic Resource Center, Yale University, New Haven, CT) were used in marker rescue assays. E. coli BL21 (sup-) was used as the host for pET28b plasmid carrying g37 alanine substitution mutants and mutant libraries. The E. coli XL10-Gold cells (Agilent Technologies, Santa Clara, CA) or DH5α cells (New England BioLabs, Ipswich, MA), were used for initial transformation and maintenance of recombinant constructs. For protein expression, sequence-confirmed recombinant clones were transferred into the expression strain E. coli BL21 (DE3) (Agilent Technologies, Santa Clara, CA) or E. coli BL21 (DE3) pLysS (Stratagene, La Jolla, CA) to allow IPTG (isopropyl-β-D-thiogalactopyranoside)-induced overexpression of recombinant proteins [53 (link)]. E. coli BZB1109 (a gift from Prof. Tillman Schirmer, Biozentrum, University of Basel, Basel, Switzerland) was used to express OmpC. The T7 expression plasmids pET28b, pCDFDuet-1, pET21a, and pET30a (EMD Millipore, MA), were used as the cloning vectors. Purified phage T4 genomic DNA was used as a template to amplify T4 g37 and its mutants.
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5

Recombinant Transketolase Purification and Characterization

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Wild-type transketolase with an N-terminal His6-tag was expressed in E. coli XL10-gold cells (Agilent Technologies Ltd) from the plasmid pQR791. The resulting cell pellet was lysed and purified as described previously37 (link). Purified transketolase was ultrafiltrated four times using Amicon Ultra-4 10k MWCO centrifugal filter to remove excess imidazole and cofactors and subsequently dialysed overnight at 4 °C in 50 mM Tris-HCl, pH 7.0 to obtain apo-TK. Protein concentration was determined by absorbance at 280 nm in 6 M Guanidine-HCl and 20 mM Sodium Phosphate, pH 6.5. Absorbance was measured using a Nanodrop spectrophotometer, assuming a monomeric molecular weight of 73035.5 g mol−1 and an extinction coefficient of 92630 L mol−1 cm−1.
Series of 2x concentrated cofactor solutions were prepared and purified TK was added to a final concentration of either 0.05 mg/mL or 0.2 mg/mL. The samples were incubated at 22 °C for 45 minutes to allow TK-TPP binding to reach equilibrium.
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6

Protein Modification and Characterization

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All consumables, solvents and reagents were purchased from Sigma/Merck unless stated otherwise. NHS–PCB–Biotin was purchased from Ambergen and stored in dry dimethylformamide at −80 °C. DreamTaq DNA polymerase master mix, TR-dextran (10 kDa) and 25 µl gene frames were purchased from Thermo Fisher Scientific. PURExpress and all other enzymes were purchased from New England Biolabs. E. coli XL10-Gold cells were purchased from Agilent. Egg PC was purchased from Avanti Polar Lipids. The 1 mm diamond drill bit was purchased from Eternal Tools. The M365L2-C5 UV lamp was purchased from Thorlabs. Standard DNA oligonucleotides were synthesized by integrated DNA technologies. Photomasks were designed using AutoCAD and purchased from JD Photodata. Amine-modified DNA oligonucleotides were synthesized by ATD-Bio. pMAT–mNG was synthesized by GeneArt. pSB1A3–bjaR–gfp was a gift from K. Haynes (Arizona State University). pET24a was a gift from B. Davis (University of Oxford). Monovalent streptavidin was a gift from M. Howarth (University of Oxford). All DNA sequences can be found in Supplementary Data.
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7

Construction of Optogenetic Vectors

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Cassettes were introduced in pcDNA3.1-(Invitrogen/Life Technologies) to generate the vectors named pOVC1-3 (optogenetic vector core 1-3, Figure S4). A XmaI restriction site was removed from the backbone using site-directed mutagenesis (oligonucleotides 1 and 2, Table S2). Inverse polymerase chain reactions (PCR) (oligonucleotides 3 and 4, 5 and 6, and 7 and 8) were applied to remove the vector multiple cloning site and create ABC (pOVC1), ACB (pOVC2) and BAC (pOVC3) cassettes. In the inverse PCR procedure, PCR products were digested with DpnI, digested with EcoRI, XmaI or AgeI (NEB), respectively, ligated for 3 h at room temperature (RT) or overnight at 4°C using T4 ligase (Promega), and propagated in E.coli XL10 Gold cells (Agilent). All cassettes contain Kozak sequences, start codons and stop codons (for backbone ABC, the stop codon was introduced using sitedirected mutagenesis in a separate reaction (oligonucleotides 9 and 10)). For linker insertion, backbone pOVC1 was digested using EcoRI and BamHI. Linker fragments were generated by inverse PCR (oligonucleotides 57 and 58) or by annealing and phosphorylating single stranded oligonucleotides (59 to 64). All vector sequences (Table S3) were verified by Sanger sequencing (Micromon, Monash University) and deposited at Addgene.org.
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