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11 protocols using ptagrfp n

1

Murine KANSL2 cDNA Cloning and Tagging

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cDNA encoding the murine KANSL2 (Gene ID: 69612) was amplified from pluripotent P19 embryonal carcinoma cells with the specific primers. Forward 5-GACCATGAACAGGATTCGGA-3 and Reverse 5-ACCGGTGGACTGATAGAAGTGGG-3, containing EcoRI and AGE I sites for cloning into pGEMT vector (Promega). Insert was subcloned into pTagRFP-N (Evrogen) to generate KANSL2-RFP.
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2

Cultivation and Transfection of HEK293 and HeLa Cells

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HEK293 (ATCC no. CRL 1573) and HeLa cells (ATCC no. CCL-2) were cultivated at 37°C and 7.5% CO2 in Iscove's modified Dulbecco's medium (IMDM) (Thermo Fisher Scientific) containing 10% fetal bovine serum (Biochrom) and penicillin/streptomycin (Invitrogen). RFP (pTagRFP-N, Evrogen) and β-tub-GFP-constructs (pEGFP-Tub, BD Biosciences) were transfected into HEK293 cells via the DOTAP lipofection reagent (Roche Applied Science). After selection with Geneticin (G418, 0.5 mg/mL, Thermo Fisher Scientific) for 4 to 6 weeks, stable transfectants of HEK293 were subcloned, sorted, and screened via flow cytometry for RFP and β-tub-GFP expression. For the chlamydial infection experiments, the HEK293 cells and all of the generated transfectants were cultured in the presence of 5 μg/mL heparin without any antibiotics, including G418. Immortalized epithelial cells from newborn mice (MN-R cells) were obtained from the Collection of Cell Lines in Veterinary Medicine (CCLV) of the Friedrich-Loeffler-Institut (CCLV-RIE number 282). The epithelial African green monkey kidney cell line BGM was obtained from the National Reference Laboratory for Chlamydiosis of the Friedrich-Loeffler-Institut (CCLV-RIE number 136).
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3

CREB-Luc Reporter Assay Protocol

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CREB transcription factor activation was measured using the pCREB-Luc CREB luciferase reporter vector (Signosis, Santa Clara, CA, USA). The cells were seeded at the density of 60,000 per well of 96-well plate the day before transfection and were cotransfected with the vector and the red fluorescent protein expression vector pTagRFP-N (Evrogen, Moscow, Russia) at a 1:1 ratio using the FuGENE HD transfection reagent (Promega, Madison, WI, USA) according to the manufacturer’s protocol. The day after the transfection the cells were treated with the test substances for 3 h in a fresh medium, after which the RFP fluorescence was measured, the cells were lysed and used for the luciferase activity detection.
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4

Plasmid Constructs for Signaling Studies

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Dominant-negative (DN)-Fyn with the K299M mutation and DN-Src with the K295M mutation in pRK5 were kindly provided by Dr. Filippo Giancotti (Memorial Sloan Kettering Cancer Center, New York, NY); pTagRFP-N was from Evrogen (Moscow, Russia). The catalytically inactive mutant of full-length PKG1α containing the amino terminal regulatory region fused to GFP (G1αR-GFP) in pEGFP-N1 (Clontech) was kindly provided by Darren Browning (Georgia Regents University). The G1αR fragment was removed via digestion with EcoR1 and BamH1 (New England Biolabs), and then inserted into the multiple cloning site of DsRed2-N1 (Clontech). Mammalian expression vectors containing GluN1, GluN2A, and GluN2B were kindly provided by Stephen Traynelis (Emory University).
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5

Constructing pRSV-loxP-RFP-loxP Plasmid

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First of all, we prepared the loxP-RFP-loxP construct based on the pRC/RSV (Invitrogen)-based expression vector, pRSV-2A (RDB12341, RIKEN BioResource center). The synthetic oligonucleotides:
loxP-f3 (5′-agcttactagtataacttcgtatagcatacattatacgaagttatcg-3′) and
loxP-r3 (5′-ctagcgataacttcgtataatgtatgctatacgaagttatactagta-3′)
were annealed and cloned into the HindIII and NheI site of pRSV-2A to generate pRSV-loxP. Then, the fragment of the tag-RFP open reading frame PCR-amplified from pTagRFP-N (FP142, Evrogen) that has SpeI and NheI site on the 5′ and 3′ ends, respectively, was inserted into the NheI site of pRSV-loxP to obtain pRSV-loxP-RFP. The SpeI-NheI fragment of pRSV-loxP-RFP was cloned into the SpeI site of pRSV-loxP to complete construction of pRSV-loxP-RFP-loxP(pRSV-LRL).
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6

Cloning and Mutagenesis of NEMO

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The plasmids used to clone GSK-3β have been described [29 (link)]. The full-length cDNA of human NEMO was cloned into pTagGFP-N or pTagRFP-N (Evrogen). Site-directed mutagenesis of NEMO (serine to alanine) was performed using the QuikChange site-directed mutagenesis kit from Stratagene (La Jolla, CA, USA). The mutations were verified by DNA sequence analysis. In addition, we used the BacMan system for the transfection of GFP-tagged Lamp1 (#C10596) or Rab5 (#C10586) according to the manufacturer’s instructions (Invitrogen, Darmstadt, Germany).
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7

Plasmid Transfection and Cell Selection

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Transfection mixtures containing plasmid pEGFP-N1 (Addgene) or pTagRFP-N (Evrogen) and lipofectamine in OptiMEM were incubated 1 h at 37°C on MPR31.4, Py8119 and NIH-3T3 cells. Then, the cells were sorted by flow cytometry and selected with G418 antibiotics.
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8

Imaging Dominant Negative and Constitutively Active RhoA

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Dominant Negative (DN)-RhoA (plasmid 15901) and constitutively active (CA)-RhoA (plasmid 15900) (Nobes & Hall 1999 (link)) were obtained from Addgene (Cambridge, MA). pTagRFP-N was acquired from Evrogen (Moscow, Russia). pEGFP-Actin was obtained from Clontech (Mountain View, CA).
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9

Transfection of HEK293 cells with siRNA

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Transfection of HEK293 cells with siRNA was performed using Viromer (Lipocalyx, Halle, Germany) according to the manufacturer’s instructions. siRNA oligonucleotides were purchased from Sigma Aldrich (Sigma-Aldrich, Taufkirchen, Germany). The following siRNA sequences were used: siGSK-3β: EHU0794515, SIHK0873, SIHK0872, siGSK-3α: EHU040791, SIHK0869. The plasmids for GSK-3β have been described previously48 (link). The full-length cDNA of human NEMO was cloned into pTagGFP-N or pTagRFP-N (Evrogen). Site-directed mutagenesis of the NEMO (serine to alanine or aspartic acid) was performed using the QuikChange site-directed mutagenesis kit from Stratagene (La Jolla, CA, USA). Mutations were verified by DNA sequence analysis. Ubiquitin wild-type (Addgene plasmid 17606; Cambridge, UK) and mutated ubiquitin, Ub-K48 and Ub-K63 (Addgene plasmids 17605, 17608), were used and have been described elsewhere54 (link).
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10

Plasmid-based Fluorescent Markers for ER, Mitochondria, and DIAPH1

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Plasmid mEmerald-Calreticulin-N-16, which was used as an ER marker, was purchased from Addgene Inc. Plasmid pECFP-Mito, which was used as a mitochondrial marker, was obtained from Takara Bio. Plasmid pTagRFP-N, which was used as a vector for DIAPH1 cloning, was obtained from Evrogen Inc. A fragment containing human DIAPH1 was PCR amplified using source clone #401258087 (Open Biosystems) as a template and inserted into the vector at XhoI and AgeI sites upstream of a fluorescent protein sequence to obtain DIAPH1-RFP.
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