GIPZ™ Lentiviral Shrna
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TECHNICAL MANUAL GIPZ™ Lentiviral shRNA Product description Design information The Dharmacon™ GIPZ™ Lentiviral shRNA Library was developed in collabora- Unique microRNA-30 based hairpin design tion with Dr. Greg Hannon of Cold Spring Harbor Laboratory [CSHL] and Dr. Short hairpin RNA (shRNA) constructs are expressed as human microRNA-30 Steve Elledge of Harvard Medical School. This library combines the design (miR-30) primary transcripts. This design adds a Drosha processing site to the advantages of microRNA-adapted shRNA with the pGIPZ lentiviral vector to hairpin construct and has been shown to greatly increase gene silencing create a powerful RNA tool capable of producing RNA interference (RNAi) in efficiency (Boden 2004). The hairpin stem consists of 22 nucleotides (nt) of most cell types including primary and non-dividing cells. dsRNA and a 19 nucleotides (nt) loop from human miR-30. Adding the miR-30 loop and 125 nucleotides (nt) of miR-30 flanking sequence on either side of the GIPZ shRNA is available in glycerol stock or viral particle hairpin results in greater than 10-fold increase in Drosha and Dicer processing format. If viral particle format is purchased, begin work with of the expressed hairpins when compared with conventional shRNA designs Protocol IX – Determining Relative Transduction Efficiency. (Silva 2005). Increased Drosha and Dicer processing translates into greater shRNA production and greater potency for expressed hairpins. Important safety note Use of the miR-30 design also allowed the use of ‘rules-based’ designs for target Please follow the safety guidelines for use and production of vector-based sequence selection. One such rule is the destabilizing of the 5' end of the lentivirus as set by your institution’s biosafety committee. antisense strand, which results in strand specific incorporation of microRNA/ siRNAs into RISC. The proprietary design algorithm targets sequences in coding • For glycerol stocks of E. coli containing lentiviral plasmids, BSL1 guidelines regions and the 3' UTR with the additional requirement that they contain great- should be followed er than 3 mismatches to any other sequence in the human or mouse genomes. • For handling and use of lentiviral products to produce lentiviral particles, BSL2 or BSL2+ guidelines should be followed Each shRNA construct has been bioinformatically verified to match NCBI • For handling and use of lentiviral particle products, BSL2 or BSL2+ guide- sequence data. To assure the highest possibility of modulating the gene lines should be followed expression level, each gene is represented by multiple shRNA constructs, each covering a unique region of the target gene. Additional information on the safety features incorporated in the pGIPZ lentiviral vector and the Horizon Trans-Lentiviral Packaging System can be found on page 3. Vector information Versatile vector design Dharmacon™ GIPZ™ shRNA vectors are not compatible with Features of the pGIPZ lentiviral vector (Figures 1 and 2) that make it a versatile third generation packaging systems, due to the requirement tool for RNAi studies include: of the expression of tat, which third generation systems do not contain. We recommend the Trans-Lentiviral Packaging • Ability to perform transfections or transductions using the replication System for use with our vectors. incompetent lentivirus (Shimada 1995) • TurboGFP™ (Evrogen, Moscow, Russia) and shRNA are part of a bicistronic transcript allowing the visual marking of shRNA expressing cells. • Amenable to in vitro and in vivo applications. • Puromycin drug resistance marker for selecting stable cell lines. • Molecular barcodes enable multiplexed screening in pools horizondiscovery.com Revised versions From PowerPoint (R&D) Antibiotic resistance hCMV hCMV pGIPZ contains three antibiotic resistance markers (Table 2). R WPRE RRE tGFP IRES PuroR WPRE RRE tGFP IRES Puro Table 2. Antibiotic resistances conveyed by pGIPZ. Ψ Ψ shRNA 3 3' SIN LT Antibiotic Concentration Utility shRNA ʹ Ampicillin (carbenicillin) 100 μg/mL Bacterial selection marker SIN R R pGIPZ (outside LTRs)pGIPZ LT LT R ʹ LT 5' 5' ™ 5 Zeocin 25 μg/mL Bacterial selection marker R (inside LTRs) R Amp pUC ori SV40 ori Puromycin Variable AmMammalianpR pU selectionCori markerSV40 ori Figure 1. pGIPZ lentiviral vector. Quality control Table 1. Features of the pGIPZ vector. The GIPZ Lentiviral shRNA Library has TRpassedE through internal QC processesUBC to TRE UBC ensure high quality and low recombination (Figures 3 and 4). Vector element Utility RRE tRFP rtTA3 IRES PuroR WPRE RRE tRFP rtTA3 IRES PuroR WPRE hCMV Human cytomegalovirus promoter drives strong transgene expression Ψ 3 Ψ shRNA shRNA 3' SIN LT ʹ tGFP TurboGFP reporter for visual tracking of transduction and SIN expression pTRIPZ R pTRIPZ R LT R LT Puro Puromycin resistance permits antibiotic-selective pressure ʹ R 5 R LT 5' 5' and propagation of stable integrants IRES Internal ribosomal entry site allows expression of TurboGFP R R Ampand puromycin pUC resistance ori genesSV40 in aor singlei transcript Amp pUCori SV40 ori shRNA microRNA-adapted shRNA (based on miR-30) for Figure 3. Representative GIPZ Lentiviral shRNA clones grown for 16 hours at 30 °C. gene knockdown Plasmid was isolated and normalized to a standard concentration. Clones were then 5' LTR 5' long terminal repeat digested with SacII and run on an agarose gel with uncut plasmid. The expected band sizes are 1259 bp, 2502 bp, and 7927 bp. No recombinant products are visible. 10 kb 3' SIN LTR 3' self-inactivating long terminal repeat for increased hCMV hCMV molecular weight ladder (10 kb, 7 kb, 5 kb, 4 kb, 3 kb, 2.5 kb, 2 kb, 1.5 kb, 1 kb). lentivirus safety R R RRE cPPT/CTS tGFP IRES Puro shRNA WPRE Ψ RRE Psi packagingtGFP sequenceIRES allowsPu viralro genomeshRNA packagingWPRE using lentiviral packaging systems Ψ Ψ RRE Rev response element enhances titer by increasing 3' SIN LT 3 ʹ packaging efficiency of full-length viral genomes SIN pSMART 2.0 R pSMART 2.0 WPRER Woodchuck hepatitis posttranscriptional regulatory LT LT R element enhances transgene expression in the target cells ʹ LT 5' 5 R Amp R pUC ori SV40 ori AmpR pUCori SV40 ori Vector map U6 hPGK U6 hPGK Figure 4. Gel image of a restriction digest of clones from the GIPZ shRNA library R R RRE shRNA Puro cultured for 10 successive RRgenerationsE in an attemptshRN toA determine the tendency of the Puro pGIPZ vector to recombine. Each generation was thawed, replicated and incubated Ψ 3 Ψ 3' SIN LT overnight for 16 hours at 30 °C then frozen, thawed and replicated. This process was ʹ SIN repeated for 10 growthR cycles. After the 10th growth cycle, plasmid was isolated and R LT pLKO.1 LT normalized to a standardʹ concentration. Clones were digested with SacII and run on R pLKO.1 R an agarose gel. The pGIPZ/5 vector appears stable without showing any recombination. Expected band sizes: 1259 bp, 2502 bp, and 7927 bp. 10 kb molecular weight ladder LT RSV/5' RSV pGIPZ R (10 kb, 7 kb, 5 kb, 4 kb, 3 kb, 2.5 kb, 2 kb, 1.5 kb, 1 kb). pUC ori Amp R 11.8 kb pUCori Amp Additional safety information hCMV Historically, the greatest safety risk associated with ahCMV lentiviral delivery RRE tGFP IRES PuroR microRNA WPRE platform stems from theRR potentialE generation of recombinanttGFP IRE virusesS Pu thatro R microRNA WPRE are capable of autonomous replication. The pGIPZ Lentiviral shRNA platform minimizes these hazardsΨ to the greatest degree by combining a disabled viral Ψ 3' SIN LT genome with the proprietary Trans-Lentiviral packaging process. Starting with 3 ʹ pSMART 2.0 the HXB2 clone of HIV-1 (GenBank,pSMA AccessionRT 2. #K03455),0 the lentiviral backbone SIN R R R LT has been modified to eliminate all but the most essential genetic elements LT ʹ LT 5' 5 necessary for packaging and integration (such as 5' LTR, Psi sequences, polypu- R rine tracts, Rev responsive elements and 3' LTR). The resultant self-inactivating Drawing was createdAmp using R GeneiouspUC (http://www.geneious.com). ori SV40 ori (SIN) vector greatly reduces the probabilityAm ofp RproducingpU recombinantCori particlesSV40 ori Figure 2. Detailed vector map of pGIPZ lentiviral vector. and limits cellular toxicity often associated with expression of HIV genes. hCMV hCMV R horizondiscovery.com R ORF IRES tGFP -2a- Blast WPRE ORF IRES tGFPnuc -2a- Blast WPRE RRE nuc Multi Tag Ψ Multi Tag Ψ Cloning Site Cloning Site 3 3' SIN LT ʹ SIN pLOC R pLOC R LT LT R ʹ LT 5' 5 R Amp R pUC ori SV40 ori AmpR pUCori SV40 ori hCMV mCMV hCMV mCMV hEF1 α e s ic er hEF1α mEF1 α SMARTchoice shRNA ho Tc mEF1α omot promoters CAG AR e SMARTchoic G pr CA PGK SM PGK UBC UBC 5' LTR Ψ RRE tGFP IRES PuroR WPRE 3' SIN LTR 5ʹ LTR Ψ RRE tGFP IRES PuroR WPRE 3ʹ SIN LTR or or tRFP SMARTvector universal scaold tRFP SMARTvector2.0 universal scaold SMARTchoiceshRNA Additional safety features can be incorporated by the packaging process Table 3. Materials for plate replication. itself. Generation of pGIPZ Lentiviral shRNA particles requires a packaging Item Vendor Cat # step during which the expression construct containing the silencing sequence 2x LB Broth (low salt) Fisher Scientific BP1427500 is enclosed in a viral capsid. Gene functions that facilitate this process (such as those encoded by the structural genes gag, pol, env, etc.) are distributed Peptone, granulated, 2 kg – Difco Fisher Scientific BP9725-2 amongst multiple helper plasmids which do not contain significant regions Yeast Extract, 500 g, granulated Fisher Scientific BP1422-500 of homology. This tactic further minimizes the probability of recombination NaCl Fisher Scientific BP3581 events that might otherwise generate viruses capable of autonomous Glycerol Fisher Scientific BP2291 replication. Among commercially available lentiviral vector systems, the Carbenicillin Fisher Scientific BP2648-250 Trans-Lentiviral Packaging System offers a superior safety profile as the Zeocin Invitrogen ant-zn-5p packaging components are separated onto five plasmids.