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22 protocols using pbifc vc155

1

Bimolecular Fluorescence Complementation Assay

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Human p113 ORF (342 bp), ZRF1 cDNA (1866 bp), and BRD4 cDNA (4089 bp) were subcloned into pBiFC-VN173 or pBiFC-VC155 (Addgene), and co-transfected into tumor cells with Lipofectamine 2000 (Invitrogen) for 24 h. The fluorescence was observed with a confocal microscope (Nikon, Japan) [15 (link), 16 (link), 19 (link)].
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2

Generation of GFP- and BiFC-tagged constructs

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GFP-tagged constructs were generated by individually cloning murine full-length ELF5, STAT5A, NFIB, GR, and MED1 cDNAs into AcGFP-C1 (#54607; Addgene, Watertown, MA, USA). The Venus N-terminal domain (VN)-tagged construct was created by PCR-amplifying ELF5 from ELF5-GFP and cloning it into pBiFC-VN155 (I152L) (#27097; Addgene). Venus C-terminal domain (VC)-tagged constructs were generated by PCR-amplifying STAT5A, NFIB, GR, and MED1 from the corresponding GFP-tagged constructs and cloning them individually into pBiFC-VC155 (#22011; Addgene).
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3

Bimolecular Fluorescence Complementation Assay for SARS-CoV-2 nsp Interactions

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The full-length nsp gene fragments used in BiFC assays (listed in Table 1) were amplified by PCR using the corresponding primers listed in Supplementary Table S1, and then, respectively, inserted into vectors pBiFC-VN173 or pBiFC-VC155 (Addgene) for the expression of fusion proteins nsp-YFPN and nsp-YFPC. Human embryonic kidney (HEK) 293T cells were co-transfected in pairs with the constructs using calcium phosphate. Cells co-transfected with pBiFC-bjun-VN173 and pBiFC-bFosVC155 were used as positive control, and cells co-transfected with pBiFC-bjun-VN173 and pBiFC-bFos(deltaZIP)VC155 were set as negative control. The supernatant was replaced with fresh medium at 8 h post-transfection, and the fluorescence was examined 24 h post-transfection using a DM5000B microscope (Leica, Germany).
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4

Plasmid-based Ubiquitin Interaction Analysis

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Plasmid encoding HA‐Ubiquitin, HA‐Ubiquitin‐K48, HA‐Ubiquitin‐K48R were purchased from Addgene and used directly without modification. Plasmid encoding pBiFC‐VC155, pBiFC‐VN173, MDM2‐YFP were purchased from Addgene and used as templates for subcloning. The plasmids were constructed for this study as described in “KEY RESOURCES TABLE” (Supporting Information). All plasmid inserts were validated by sequencing at Genewiz. All siRNAs were purchased from Synbio Technologies. The sequences of the siRNA were described in “KEY RESOURCES TABLE” (Supporting Information). Cultured cells were transfected with different plasmids using Lipofectamine 2000 (Invitrogen, 11668‐019) and with siRNAs using RNAi Max (Invitrogen, 13778150) according to the manufacturer's instructions.
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5

Evaluating Protein-Protein Interactions

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Primers for p57, p53, Pcna, p21, p27, p16, Wnt6, and Wnt2 were designed using primer 5 and are listed in Table S2. For BiFC assay, p57 gene was linked with pBiFC-VC155 (Addgene, Watertown, Massachusetts, USA), while p53, Pcna, p21, p27, p16, Wnt6, and Wnt2 genes were linked with pBiFC-VN173 (Addgene) as described above. Before transfection, 1 × 105 293 T cells were plated into each well of 12-well plates. BiFC-p57-VC155 was cotransfected with BiFC-p53-VN173 (or BiFC-Pcna-VN173, BiFC-p21-VN173, BiFC-p27-VN173, BiFC-p16-VN173, BiFC-Wnt6-VN173, and BiFC-Wnt2-VN173) using TurboFect Transfection Reagent (Thermo Fisher Scientific) according the manufacturer's instructions. 6 h later, fresh culture medium was changed and the cells were further cultured for 48 h before analysis.
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6

Bimolecular Fluorescence Complementation of Oncogenes

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Human cDNAs of c‐Myc (1365 bp), LMNA (1995 bp) and LMNC (1719 bp) were inserted into pBiFC‐VN173 (containing Flag‐tag) or pBiFC‐VC155 (containing HA‐tag) from Addgene. The c‐Myc and LMNA constructs were mutated by QuikChange Multi Site‐Directed Mutagenesis Kit (Agilent) using primer sets (Table S5). Constructs were co‐transfected into tumour cells by using NeuroPorter Transfection Kit (Sigma) for a 24‐h period, while fluorescence imaging was detected using a confocal microscope.
41 (link),
42 (link),
44 (link),
45 (link)
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7

BiFC Assay for DDI2ΔUBL Interaction

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The BiFC assay was performed as described previously.67 (link) To generate plasmids expressing split Venus fragments-tagged DDI2ΔUBL, the DDI2 cDNA was cloned into pBiFC-VN173 (Addgene_22010) or pBiFC-VC155 (Addgene_22011), respectively. Both BiFC plasmids were co-transfected with a pmCherry-N1 plasmid (Clontech), which was used as an internal control. At one day after transfection, the cells were cultured without all amino acids for 3 h. The fluorescent intensities of Venus and mCherry were measured using a flow cytometer (FACSAriaII, BD Biosciences). Median fluorescence intensity (MFI) values of Venus in mCherry-positive cells were measured by flow cytometry.
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8

Visualizing MCU Complex Protein Interactions

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To visualize protein binding, plasmids were created for bimolecular fluorescent complementation (BiFC) of Venus using N-terminal (VN) and C-terminal (VC) reporter fragments as previously described (Kodama and Hu, 2010 (link)). In brief, the coding region of each cDNA (MCUR1, MCU, MICU1, EMRE and PPIF) was amplified by PCR and cloned into pBiFC-VC155 (addgene Plasmid 22011) to generate the corresponding cDNA-VC protein expressed in frame. Similarly, all the cDNAs were also cloned into pBiFC-VN155 (addgene Plasmid 27097) to generate the corresponding cDNA-VN protein expressed in frame. HeLa cells were plated in six-well plates containing 0.2% gelatin- coated glass coverslips and transfected with corresponding plasmid encoding for MCU complex component proteins fused with -VN and -VC reporter fragments. After 36 hours, cells were loaded with Tetramethylrhodamine, methyl ester (TMRM; 100 nM) for 30 min at 37°C for mitochondrial staining. Note: Basal autofluorescence was observed in non-expressing cells that was considered negative. Image acquisition was performed using a Carl Zeiss 510 confocal microscope using a 63× oil objective with excitation at 514 and 561 nm respectively. Intensity profile were created using line scan for relative fluorescence of BiFC/TMRE using Carl Zeiss ZEN 2010 Imaging Software.
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9

Fluorescent Protein Interaction Assay

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Human EWSR1 cDNA (1,971 bp) and MAZ cDNA (1,482 bp) were subcloned into BiFC vectors pBiFC‐VN173 and pBiFC‐VC155 (Addgene), and co‐transfected into tumor cells for 24 h. The fluorescence emission was observed under a confocal microscope, with excitation and emission wavelengths of 488 and 500 nm, respectively (Kerppola, 2008).
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10

Bimolecular Fluorescence Complementation

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Human ARMC12 cDNA (1104 bp) or RBBP4 cDNA (1278 bp) was respectively subcloned into pBiFC-VN173 and pBiFC-VC155 (Addgene, Cambridge, MA). Mutation of ARMC12 or RBBP4 was undertaken with GeneTailorTM Site-Directed Mutagenesis System (Invitrogen) and PCR primers (Supplementary Table 7). After co-transfection of recombinant constructs using Lipofectamine 3000 (Invitrogen) for 24 h, tumor cells were grown for additional 10 h at 37 °C. Under a confocal microscope, the fluorescence emission was detected (488 and 500 nm as excitation and emission wavelengths, respectively).
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