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Pcdna3 expression vector

Manufactured by Thermo Fisher Scientific
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The pcDNA3 expression vector is a commercially available plasmid used for the expression of recombinant proteins in mammalian cell lines. It contains a cytomegalovirus (CMV) promoter for high-level transgene expression and a neomycin resistance gene for selection of transfected cells.

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40 protocols using pcdna3 expression vector

1

Recombinant Plasmid Generation and mRNA Transcription

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The sequences encoding recombinant full-length LMP1, LMP2a and GFP were cloned into the pcDNA3 expression vector (Invitrogen, Grand Island, NY, USA). The purified plasmids (LMP1-pcDNA3, LMP2a-pcDNA3 and GFP-pcDNA3) were linearized by digestion with the restriction enzyme Sma I and purified using the Nucleospin Gel and PCR Clean-up Kit (Macherey-Nagel, Duren, Germany). mRNAs were transcribed from the linearized plasmids using an Ambion mRNA T7 Ultra Kit (Life Technologies) according to the manufacturer’s instructions.
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2

Cloning and Mutagenesis of SOX9 and CEACAM1

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SOX9 expression vector was purchased from the plasmID Repository at Harvard Medical School (clone HsCD00004049). SOX9 cDNA was amplified from this vector and inserted into a pcDNA3 expression vector (Invitrogen, Carlsbad, CA, USA) using HindIII and XhoI restriction enzymes (New England Biolabs, Ipswich, MA, USA). DNA from melanoma cells for cloning of the CEACAM1 promoter was purified using GenElute Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich, St. Louis, MO, USA). Promoter fragments containing the full or partial putative promoter of CEACAM1 were amplified and cloned into pGL4.14 reporter vector (Promega, Madison, WI, USA) using XhoI and HindIII sites. Point mutations and deletions were introduced into the various constructs using specific primers, DNA synthesis with KOD Hot Start Polymerase (Merck Millipore, Darmstadt, Germany) and ultimately DpnI (New England Biolabs, Ipswich, MA, USA) digestion at 37°C for 1 hour. The full sequences of all primers used are detailed in Supplementary Table 1.
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3

Cloning and Expression of IκBα and MAP3K14

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The pCMV-IκBαm expression vector which contains serine to alanine mutations at residues 32 and 36 of IκBα was purchased from Clontech (Moutain View, GA, USA). The MAP3K14 expression vector was constructed by cloning the MAP3K14 cDNA (MGC:45335; Invitrogen) after digestion with Eco RI and Xho I into the pcDNA3 expression vector (Invitrogen).
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4

Site-Directed Mutagenesis of Human MC4R

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Receptor mutagenesis was performed as previously described.47 (link)–49 (link), 54 The human WT N-terminal FLAG-tagged MC4R cDNA (Supplemental Figure 1A) was generously provided by Dr. Robert Mackenzie59 (link) and was sub-cloned into the pBluescript plasmid (Stratagene) for subsequent mutagenesis. Site directed hMC4R mutagenesis was performed using a polymerase chain reaction (PCR) based strategy, using the Pfu turbo polymerase (Stratagene). Complementary sets of primers were designed containing nucleotide base pair changes resulting in the modified amino acids (Supplemental Figure 1B). Upon completion of the PCR reaction (95 ºC 30 s, 12 cycles of 95 ºC 30 s, 55 ºC 1 min, 68 ºC 9 min), the product was purified (Qiaquick PCR Purification Kit, Qiagen) and eluted in water. Subsequently, the sample was cut with Dpn1 (Invitrogen) to eliminate any methylated WT DNA, leaving only nicked circularized mutant DNA. The mutant hMC4R DNA was transformed into competent DH5α E. coli cells and single colonies were selected. The presence of the desired mutation was verified by DNA sequencing. The plasmid DNA containing the mutant was excised and sub-cloned into the HindIII/XbaI restrictions sites of the pCDNA3 expression vector (Invitrogen). Complete FLAG-MC4R sequences were confirmed free of PCR nucleotide base errors by DNA sequencing (University of Florida sequencing core facilities).
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5

Characterization of CLN1 Mutations in Mediterranean Patients

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We focused our attention on CLN1 mutations described in Mediterranean patients affected by classical and variant CLN1 disease. Specifically, we selected three different missense mutations (c.665T>C/p.L222P, c.541G>A/p.V181M and c.541G>T/p.V181L), a deletion of the second exon (c.125_235del/p.G42_E78del) in which the ORF is maintained and a one-base insertion (c.169dupA/p.M57Nfs*45) predicting a frameshift, and a premature stop codon at residue 101 (Santorelli et al., 1998 (link)). Wild-type and mutated CLN1 cDNAs (NM_000310) were inserted into pcDNA3 expression vector (Invitrogen, Life Technologies [LT]) by PCR methods. The sequences of CLN1 constructs were confirmed by direct sequencing using BigDye Terminator v3.1 Cycle Sequencing Kit (Applied Biosystems, LT), on an ABI3130xl automatic DNA Analyzer. SH-SY5Y cells were plated 1 day before transfection at 80% confluence in 35 mm dishes, and then transfected with 250 ng of cDNAs per dish using lipofectamine method (Applied Biosystems, LT) following the manufacturer’s instructions. Clones which stably overexpressed the different CLN1 cDNAs were finally isolated through antibiotic selection with 600 μg/ml geneticin (G418, Gibco, LT). Cells overexpressing the empty pcDNA3 vector (hereafter also referred as mock) served as a control (Table 1).
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6

Establishing Stable Cell Lines for IL-6, STAT3, and PIAS3 Studies

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Full-length human IL-6, STAT3, and PIAS3 expression vectors were constructed as previously described [26 (link),27 (link)]. Briefly, the human STAT3 (pcDNA-STAT3) and PIAS3 (pcDNA-PIAS3) expression vectors were constructed by cloning the STAT3 cDNA vector (MCG: 4909141) and the PIAS3 cDNA vector (MGC: 3528679), respectively, into the pcDNA3 expression vector (Invitrogen, Carlsbad, CA, USA). The human IL-6 expression vector (pcDNA-IL-6) was constructed by cloning the IL-6 cDNA vector (MCG: 9215) after digestion with Eco RI and Not I into the pcDNA3.1/Zeo expression vector (Invitrogen). The human HO-1 expression vector was constructed by cloning a full-length HO-1 cDNA (MGC:1723; Invitrogen) into the pcDNA3.1/Zeo expression vector (Invitrogen) with Eco R1 sites. The HO-1 or IL-6 expression vector was transiently transfected into HepG2 or Hep3B cells, respectively, by electroporation, as previously described [28 (link)]. Cells were maintained in RPMI medium with 10% FCS and 100 μg/mL of Zeocin (Invitrogen). HO-1 or IL-6 expression in resistant colonies (HepG2-HO1, Hep3B-HO1, and HepG2-IL-6) was evaluated by immunoblot, RT-qPCR, or ELISA, as described below. The mock-transfected HepG2 cells (HepG2–DNA) and Hep3B (Hep3B–DNA) were transfected with the control pcDNA3.1/Zeo expression vector and also selected by Zeocin.
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7

Establishment of Stable CHO Cell Line Expressing ARMS1-PK2

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The oligonucleotides used in this study were synthesized by Genotech (Daejeon,
Korea). The cloning vector (pGEMT-T easy) was purchased from Promega (Madison,
WI, USA). The pcDNA3 expression vector, pCMV-ARMS1-PK2 expression vector,
Freestyle MAX reagent, FreeStyle CHO-suspension (CHO-S) cells and AssayComplete
medium were purchased from Invitrogen (Carlsbad, CA, USA). The PathHunter
Parental CHO-K1 cell line expressing β-arrestin 2 was
purchased from DiscoveRx (San Diego, CA, USA). The pCORON1000 SP VSV-G-tag
expression vector was purchased from Amersham Biosciences (Piscataway, NJ, USA).
The PMSG-ELISA kit was purchased from DRG International (Mountainside, NJ, USA).
Restriction enzymes and DNA ligation reagents were purchased from Takara Bio
(Shiga, Japan). Fetal bovine serum (FBS) was obtained from HyClone Laboratories
(Logan, UT, USA). The cAMP Dynamic 2 immunoassay kit was purchased from Cisbio
(Codolet, France). CHO-K1 cells and HEK 293 cells were obtained from the Korean
Cell Line Bank (KCLB, Seoul, Korea). The QIAprep-Spin plasmid kit was purchased
from Qiagen (Hilden, Germany). All other reagents were obtained from
Sigma-Aldrich (St. Louis, MO, USA).
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8

Establishing Rat Mgat5 Expressing Clones

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Rat Mgat5 cDNA (Shoreibah et al. 1993 (link)) was subcloned into the EcoRI site of the pcDNA3 expression vector (Invitrogen, San Diego, CA). Lec4 cells were plated on 35 mm cell culture dishes and grown in α-MEM medium supplemented with 10 % fetal calf serum. Plasmid DNA (1 μg per 35 mm culture dish) was transfected into Lec4 cells, using Fugene™ 6 transfection reagent (Boehringer Mannheim, Germany) according to the manufacturer's protocol. Following transfection, clonal cell lines were established by selection for G418 resistance and tested for cell surface expression of β1,6 GlcNAc-branched N-glycans using digoxigenin-conjugated leukoagglutinating Phaseolus vulgaris lectin (dig L-PHA; Boehringer Mannheim, Germany) as described below. The positive clonal cell lines were designated Lec4 GnTV-N5, Lec4 GnTV-N10, and Lec4GnTVN30. Lec4 cells were mock-transfected with the pcDNA3 expression vector as described above, and clonal cell lines were established and designated Lec4 pcDNA3.
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9

Genetic Constructs for Cell Biology

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The constructions used for this study, namely 3xHA-SIVA-1, 3xHA-ΔSIVA-1, 3xFLAG-FAIM-L, 3xHA-FAIM-L, 6xMyc-XIAP and YFP, were expressed under the control of a cytomegalovirus constitutive promoter in the pcDNA3 expression vector (Invitrogen). 3xFLAG-SIVA-1 plasmid was kindly provided by Dr. Ulrike Resch (Medical University of Vienna). Lentiviral plasmids for this study were cloned into pEIGW. Short hairpin RNA (shRNA) targeting SIVA-1 was cloned into the pLVTHM vector, and a scrambled sequence was used as a control.
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10

Recombinant Expression of Rare CFI Variants

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For recombinant expression studies, rare coding variants in CFI with a minor allele frequency (MAF) of <1.5% were selected based on Geerlings et al. (14 (link),16 (link)). All 126 variants included are summarized in Supplementary Material, Table S1 and the distribution throughout FI is shown in Figure 1. MAF was obtained from the genome aggregation database (https://gnomad.broadinstitute.org/, on 18.10.2019). Full-length CFI cDNA (NM_000204.4, on GRCh37) was cloned into a pcDNA3 expression vector (Invitrogen, USA) as described (40 (link)). Variants were introduced using the Q5 site-directed mutagenesis kit (New England Biolabs, USA). Mutagenesis primers were designed using http://nebasechanger.neb.com/ or by designing overlapping primers including the desired nucleotide change. All mutagenesis primers are listed in Supplementary Material, Table S3. Sanger sequencing of the whole CFI insert, using the BigDye™ Terminator v1.1 Cycle Sequencing Kit (Applied Biosystems, USA), was performed to confirm presence of the desired variant and absence of additional unwanted changes introduced by PCR.
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