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Tracrrna atto 550

Manufactured by Integrated DNA Technologies
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The TracrRNA-ATTO 550 is a laboratory reagent designed for use in CRISPR-Cas9 gene editing experiments. It is a synthetic trans-activating CRISPR RNA (tracrRNA) molecule labeled with the ATTO 550 fluorescent dye. The primary function of this product is to serve as a component in CRISPR-Cas9 systems, where it assists in the guidance and activation of the Cas9 endonuclease enzyme during the gene editing process.

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7 protocols using tracrrna atto 550

1

CRISPR-Cas9 Genome Editing and Protein Detection

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Alt-R CRISPR-Cas9 reagents (S.p. HiFi Cas9 Nuclease V3, Electroporation enhancer, tracrRNA ATTO550, and crRNAs) and ssODN (HDR Donor Oligos) were purchased from Integrated DNA Technologies. PCR primers were obtained from GeneriBiotech. Nano-Glo HiBiT Lytic Detection System and Nano-Glo HiBiT Extracellular Detection System were purchased from Promega. Antibodies: mouse anti-human CFTR antibodies (569, TJA9; CF Foundation), donkey anti-mouse IgG (H + L) Highly Cross-Adsorbed Secondary Antibody (Alexa Fluor 647; Invitrogen). siRNA: CFTR Human siRNA Oligo Duplex (Locus ID 1080; Origene), RAB5 (RAB5A) Human siRNA Oligo Duplex (Locus ID 5868), and RAB11 Human siRNA Oligo Duplex (Locus ID 8766).
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2

CRISPR-Cas9 Genome Editing in Medaka Fish Cells

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Recombinant S. pyogenes Cas9 Nuclease 3NLS, crRNA, tracrRNA ATTO 550 and none-targeting carrier DNA were obtained from Integrated DNA Technologies (Skokie, IL, USA). To form crRNA: tracrRNA complex, 5 μl 200-μM crRNA and 5 μl 200-μM tracrRNA were mixed and heated at 95°C for 5 min. The mixture was then incubated at room temperature for 30 min. To form RNP complex, 2.1 μl DPBS, 1.2 μl crRNA: tracrRNA complex and 1.7 μl Cas9 nuclease (61 μM) were mixed and incubated at room temperature for 10-20 min. For RNP electroporation, 1 million medaka fish cells at 90% confluence were trypsinized and washed in 1 ml DPBS twice by spin-down and resuspension. Washed cells were suspended in 94 μl DPBS and 5 μl RNP complex and 1 μl 100 μM carrier DNA were added by gentle pipetting. The mixture was transferred to sterile electroporation cuvette with 0.2 cm gap (Bio-Rad Laboratories) and electroporated with 220 V and 5 ms by the Gene Pulser Xcell Electroporation Systems (Bio-Rad). At 24 h post electroporation (hpe), culture medium was changed and the cells were cultured for another 7 days before genotyping.
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3

Fluorescent RNP Complex Isolation

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After the transfection (24 h), the P19 cells labeled with tracrRNA-ATTO-550 (Integrated DNA Technologies, Coralville, IA, USA) were isolated using fluorescence-activated cell sorting (FACS). Cells treated with a fluorescence RNP complex, but without a transfection reagent, were used as a control to set the gate during the cell sorting. The flow cytometric analysis was performed on a FACSAria (BD Biosciences, San Jose, CA, USA) using Cell Quest software (BD Biosciences, San Jose, CA, USA) in the Department of Immunology at the University of Warsaw, Poland.
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4

CRISPR/Cas9-Mediated SOX2 Knockout in CWR-R1 Cells

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To generate CRISPR/Cas9-mediated SOX2KO cell lines, parental CWR-R1 cells were co-transfected with pT2-EF1a-Cas9-P2A-puro and pCMV(CAT)T7-SB100 (#34879, Addgene; Watertown, MA) using Lipofectamine 2000 (Invitrogen) to introduce Cas9 expression. Stable constitutive Cas9 expression was accomplished by SB100 transposase integration of EF1a-Cas9-P2A-puro. Cas9-expressing cells were selected for and maintained with puromycin (1 mg/mL, Invitrogen) 48 h after transfection. Constitutive Cas9 expression was confirmed by western blot (# 14697, Cell Signaling Technologies) after 1 week of puromycin selection. Two custom crRNAs (Integrated DNA Technologies; Coralville, IA) targeting the N-terminus of SOX2 were selected using CHOPCHOP software (https://chopchop.cbu.uib.no) (SOX2 crRNA #1: 5’-CGGGCCCGCAGCAAACTTCG-3’, SOX2 crRNA #2: 5’-CGCCCGCATGTACAACATGA-3’) and were individually complexed with tracrRNA-ATTO 550 (#1075927, Integrated DNA Technologies) at a 1:1 ratio immediately before transfection. A final concentration of 10 nM crRNA:tracrRNA duplexes were transfected into CWRR1-Cas9 cells using siLentFect Lipid Reagent for RNAi (#1703360, BioRad) following manufacturer guidelines. Limited dilution was performed to isolate three clonal knockout cell lines, and successful knockout of SOX2 was validated by western blot (anti-SOX2(D6D9), #3579, Cell Signaling Technologies).
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5

CRISPR-Cas9 Targeting Immune Checkpoint Genes

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Specific crRNAs (0.1 mmol/L each; PD1_crRNA1, TIM3_crRNA2, LAG3_crRNA3; Integrated DNA Technologies, IDT, Coralville, IA, USA) and universal transactivating crRNA (tracrRNA-ATTO™550, 0.1 mmol/L; Integrated DNA Technologies, IDT, Coralville, IA, USA) were mixed at equimolar concentrations and heated at 95 °C for 5 min in a ThermoMixer® (Eppendorf, Hamburg, Hamburg, Germany). The mixture was then cooled down until room temperature (RT) was reached. Precomplexing of Cas9 (30 pmol/μL, TrueCut™ Cas9 Protein v2, Thermo Fisher Scientific, Waltham, MA, USA, #A36498) endonuclease with all crRNA/tracrRNA complexes (80 pmol/μL of PD1_crRNA1/tracrRNA, TIM3_crRNA2/tracrRNA, and LAG3_crRNA3 /tracrRNA) was completed by mixing and incubating for 10 min at room temperature. crRNA/tracrRNA/Cas9 mixture was electroporated into 2.5 × 105 EL4 lymphoma cell line, 4 × 106 MH and OT CD8+ T cells by 4D-Nucleofector® X Unit (Lonza, Basel, Switzerland). As control of the transfection (T.C.) CD8+ T cells were transfected with a mock crRNA/trRNA/Cas9.
For MH and OT-1 CD8+ T cells nucleofection was performed 1 week after CD3/CD28 mediated activation. EL4, MH, and OT-1 CD8+ T cells positive for ATTO™550 were sorted and EL4 positive cells were cultured in RPMI 10% FBS, while MH and OT-1 CD8+ T cells in TCM with added IL-7 and IL-15.
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6

CRISPR/Cas9-Mediated SOX2 Knockout in CWR-R1 Cells

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To generate CRISPR/Cas9-mediated SOX2KO cell lines, parental CWR-R1 cells were co-transfected with pT2-EF1a-Cas9-P2A-puro and pCMV(CAT)T7-SB100 (#34879, Addgene; Watertown, MA) using Lipofectamine 2000 (Invitrogen) to introduce Cas9 expression. Stable constitutive Cas9 expression was accomplished by SB100 transposase integration of EF1a-Cas9-P2A-puro. Cas9-expressing cells were selected for and maintained with puromycin (1 mg/mL, Invitrogen) 48 h after transfection. Constitutive Cas9 expression was confirmed by western blot (# 14697, Cell Signaling Technologies) after 1 week of puromycin selection. Two custom crRNAs (Integrated DNA Technologies; Coralville, IA) targeting the N-terminus of SOX2 were selected using CHOPCHOP software (https://chopchop.cbu.uib.no) (SOX2 crRNA #1: 5’-CGGGCCCGCAGCAAACTTCG-3’, SOX2 crRNA #2: 5’-CGCCCGCATGTACAACATGA-3’) and were individually complexed with tracrRNA-ATTO 550 (#1075927, Integrated DNA Technologies) at a 1:1 ratio immediately before transfection. A final concentration of 10 nM crRNA:tracrRNA duplexes were transfected into CWRR1-Cas9 cells using siLentFect Lipid Reagent for RNAi (#1703360, BioRad) following manufacturer guidelines. Limited dilution was performed to isolate three clonal knockout cell lines, and successful knockout of SOX2 was validated by western blot (anti-SOX2(D6D9), #3579, Cell Signaling Technologies).
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7

CRISPR-Cas9 Genotyping Protocol

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Primers, ssODN HDR donor templates, quantitative real-time PCR assays (human CFTR, Hs.PT.58.28207352; human TBP, Hs.PT.58v. 39858774; human GusB, Hs.PT.58v.27737538; rat GusB, Rn.PT.58. 35199448), and Alt-R® CRISPR Cas9 reagents (S.p. Cas9 Nuclease 3NLS; crRNA; tracrRNA; and tracrRNA, ATTO 550 ) were purchased from Integrated DNA Technologies (IDT). SNP discrimination assays were custom ordered from IDT [F508del: primer 1 5′-ATTATGCCT GGCACCATTA-3′; primer 2 5′-TGATGACGCTTCTGTATCTA-3′; probe (FAM) 5′-AATATCATCTTTGGTGTTTCCT-3′; probe (HEX) 5′-AATATC ATTGGTGTTTCCTATGA-3′] or purchased from Thermo Fisher Scientific (W1282/X assay: C__32545014; G542/X assay: C__11399026; M470/V470 assay: Custom TaqMan SNP Genotyping Assay, human). WT (ND03719), W1282X (GM11723), and G542X (GM11496) samples for genotype control were purchased from Coriell Biorepository. Geneticin (G418) was purchased from Sigma-Aldrich (A-1720) and SMG1i was custom-synthesized by Kalexsyn (Kalamazoo, MI).
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