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12 protocols using pegfp n1 vector

1

Plasmid construction and transfection

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The cDNA sequences encoding ATP5B or DRP1 were amplified by PCR using the oligonucleotide primers (Genomics, Hsinchu, Taiwan). The amplified fragments were cloned into a pPAGFP-N1 vector (RRID: Addgene_11909) or pCMV-HA-N vector (Clontech Cat# 635690), respectively. MOM-GFP plasmid containing mitochondrial targeting sequence of Tom70 fused to pEGFP-N1 vector was a gift from Josef Kittler (RRID: Addgene_127633)95 (link). Mitochondrial targeting sequence from subunit VIII of human cytochrome C oxidase was amplified from DsRed2-Mito-7, a gift from Michael Davidson (RRID: Addgene_55838) by PCR, and cloned into pEGFP-N1 vector backbone to be Mito-GFP plasmid. All clones were verified by sequencing (Genomics). The Escherichia coli DH5α strain was used as the competent cell for the transformation of these constructs. The QIAGEN Plasmid Midi Kit (QIAGEN Cat#12143) was used for the purification of plasmids, and the concentration of the purified plasmids was determined using the NanoDrop ND-1000 (NanoDrop Technologies, Montchanin, DE). Plasmids were transfected into cells using jetPRIME (Polyplus-transfection Cat#114-15) according to the instructions provided by the manufacturer, and the transfected cells were incubated for at least 24 h before further experiments.
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2

Exosome tracking via CD63-EGFP

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CD63 cDNA was amplified and cloned into the pEGFP‐N1 vector (Addgene, MA, USA) as described previously (Ye et al., 2020). Then, plasmid for CD63‐EGFP expression was transfected into cells. After 24 h, exosomes were isolated from the conditioned medium and intravenously administered to mice.
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3

Quantification of miR-30b-5p expression

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To quantify miR-30b-5p expression, total RNA enriched with small RNA was extracted using the mirVana™ miRNA Isolation Kit (Thermo Fisher Scientific) and analyzed by RT-qPCR using miRNA TaqMan® probe (Assay ID: 000602, miRbase accession# MI0000441, mature miRNA sequence: UGUAAACAUCCUACACUCAGCU) from Applied Biosystems/Thermo Fisher Scientific). mir-30b-5p mimic (Assay ID: MC10986), miRNA mimic negative control (#4464058), miR-30b-5p inhibitor (Assay ID: MH10986), Mir-30b-5p inhibitor negative control (#4464076) were all purchased from Applied Biosystems/Thermo Fisher Scientific. SMCs were transfected with 80 nM of the indicated mimic, mimic negative control, miRNA inhibitor, or inhibitor negative control using the Neon® transfection system (MPK-5000; Invitrogen, Waltham, MA). SMCs were microporated using the following parameters: pulse voltage: 1,300 V; pulse width: 20 ms; pulse number: 2; the tip type: 10 μl) and then cultured for 24 hr. The transfection efficiency was ∼51% with 2% cell death as determined using the pEGFP-N1 vector (#6081-5; addgene). Transfections with the indicated mimics and inhibitors did not significantly modulate SMC shape, viability, or adherence (trypan blue dye exclusion; data not shown).
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4

Lentiviral expression of VCP variants

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Human VCP(wt)-GFP in the pEGFP-N1 vector was purchased from Addgene (#23971) (Tresse et al., 2010 (link)). VCP was digested out of pEGFP-N1 with BglII (5′) and Age I (3′) and cloned into the same sites in the lentiviral pFLRu-FH vector to generate VCP(wt)-FLAG-6His (Feng et al., 2010 (link)). S784A and S784D were introduced using QuickChange site-directed mutagenesis. S784A sense primer: TGGAGCTGGCCCCGCTCAGGGCAGTGGA; antisense primer: TCCACTGCCCTGAGCGGGGCCAGCTCCA. S784D sense primer: TGGAGCTGGCCCCGATCAGGGCAGTGGA; antisense primer: TCCACTGCCCTGATCGGGGCCAGCTCCA. Two human VCP-specific shRNAs in the pLKO.1 vector were purchased from the RNAi consortium at the Genome Institute at Washington University: CCTGATGTGAAGTACGGCAAA (#1) and AGGGAGGTAGATATTGGAATT (#2). To confer shRNA resistance, multiple synonymous mutations were introduced within the target sequences of VCP by Genewiz: CCAGACGTCAAATATGGTAAG (#1) and CGCGAAGTTGAGATAGGAATT (#2). Two human Pfn1-specific shRNAs were described previously (Diamond et al., 2015 (link)).
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5

Labeling DNA with Biotin and Digoxigenin

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A commercially
available short biotinylated and digoxigenin (DIG) labeled 3 kb DNA
(Lumicks) was subcloned using 5′XhoI and 3′EcoRI (NEB) into the pEGFP-N1 vector (Addgene #6085-1). The primers
(IDT) used to amplify the DNA sequence by PCR were:
Forward:
5′-AAACTCGAGGGCAGGTGAAGGACTCCTTCGGC-3′,
Reverse:
5′-AAAAAGAATTCCAGTTCGCTGCACTGCTCAATGCG-3′.
After employing the restriction enzyme-based cloning technique,
the construct was transformed into chemically competent DH5α Escherichia coli cells (Thermo Fisher). The success
of the procedure was determined by Sanger sequencing (ZABAM Instrumentation
and Service sequencing unit at Tel Aviv University), and this construct
was used as a PCR template for further DNA amplifications.
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6

Visualizing Intracellular Signaling Pathways

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Flag-REGγ was previously generated [36 (link)]. GFP-PKAca was generated in pEGFP-n1-vector (Addgene). Antibodies were purchased from Invitrogen (PA28γ), Cell Signaling (FoxO1, Phospho-FoxO1/Ser256, Thr24, Ser319), Sigma (β-actin, M2 anti-Flag), Santa Cruz (PKAα cat, HA, GFP), GeneTex (E-Selectin, VCAM-1). Other purchased reagents include VEGF-A165 (PeproTech Inc), cycloheximide (Amresco). All the experiments shown in the study were repeated at least three times.
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7

Plasmid Construction for Protein Expression

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ARRDC1-GFP expression construct was made previously9 (link). pcDNA3-p53 expression construct was made by cloning full-length DNA fragment of wild-type p53 into the pcDNA3.1(+) vector (between the EcoRI and XhoI sites). ARRDC1-p53 fusion construct was made by cloning the full-length ARRDC1 DNA into pcDNA3-p53 (between the NheI and EcoRI sites) upstream of the p53 gene. New constructs were confirmed by direct DNA sequencing. To generate ARRDC1-TAT construct, the DNA sequence of ARRDC1 was PCR amplified followed by insertion into pcDNA3 vector to obtain pcDNA3-ARRDC1 construct. The DNA sequence of TAT (48–65 aa) was synthesized, annealed, and inserted at the C-terminus of ARRDC1. The DNA sequence of TAR (1–63 base pairs) was synthesized, annealed, and inserted at the 5′ end of EGFP in the pEGFP-N1 vector (Addgene) to obtain the TAR-EGFP construct. Alternatively, the TAR region was inserted at the 5′ end of p53 in the pcDNA3-p53 construct to obtain the TAR-p53 construct. 2WW-Cas9-anti-GFP and 4WW-Cas9-anti-GFP were constructed by cloning either two or four WW domains from ITCH into the AgeI site of the px-330 vector (Addgene).
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8

Cloning and Transfection of wtp53 and p53R248Q

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The wild-type p53 (wtp53) and p53R248Q mutation (p53R248Q) plasmids were constructed in house. The full-length wtp53 and p53R248Q sequences were made from A2780 and OVCAR3 cells. Total cDNA was amplified by using KAPA HiFi DNA polymerase (KAPABIOSYSTEMS). The primer sequences were the following: 5′-CTCGAGGCCTGAGGTTGGCTCTGACT-3′ and 5′-GAATTCGGCACAAACACGCACCTCAA-3′. The PCR products were constructed into pJET1.2/blunt cloning vector (Fermentas) and sub-cloned into pEGFP-N1 vector (Addgene). The final plasmids were sequence verified. Cells were transfected with plasmids at a final concentration of 1 μg/mL using jetPRIME (Polyplus) following the manufacturer’s protocols.
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9

Cloning of USP3 Fusion Constructs

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To create the USP3–GFP and USP3ZnF(1–110)–GFP expression constructs, USP3 complimentary DNA (Source Bioscience) was amplified with the use of the indicated primers (Supplementary Table 4) and cloned in-frame into the BamHI and XhoI restriction sites of the pEGFP-N1 vector (Addgene).
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10

Transfection of PASMCs with GFP-NCL

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The plasmid GFP-NCL was a gift from Michael Kastan (Addgene plasmid #28176; http://n2t.net/addgene:28176; RRID: Addgene_28176) [61 (link)]. PASMCs were transfected with 1 μg of the GFP-NCL or the empty pEGFP-N1 vector (Addgene, Watertown, MA, USA) using the P1 Primary Cell 4D-NucleofectorTM X kit (Lonza, Basel, Switzerland) according to the manufacturer’s protocol.
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