Supplementary Figure 1 NgAgo binds ssDNA guide in a one-guide-faithful manner. NgAgo-expressing plasmid was transfected to 293T cells and then NgAgo was purified and used in an in vitro plasmid cleavage assay. The NgAgo derived from the cells co-transfected with target-complementary guide (FW, Lane 4) but not that derived from the cells cotransfected with a random guide (NC, Lane 5) could cause DSBs and linearize the plasmid. The NgAgo derived from the cells without guide co-delivery could not cleave the target even if the purified NgAgo was later co-incubated with the FW guide (Lane 3). After NgAgo binds to an ssDNA, it will not swap its bound guide (here is NC) to another free guide (here is FW) at 37℃ (Lane 6). Representative figure of 3 independent experiments. Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary Figure 2 Guide reloading process at 55℃ impairs endonuclease activity of NgAgo. NgAgo was purified from E.Coli. and then co-incubated with 5’ phosphorylated ssDNA guide at 37 ℃ or 55℃ for 1 hour or 72 hours. NgAgo was then subject to a plasmid cleavage assay to test its endonuclease activity. It shows that 55℃ for 1 hour changes the activity of NgAgo to a nickase and 55℃ for 72 hours completely deprived of its activity. SC, supercoiled; Lin, linearized; OC, open circular. Representative figure of 3 independent experiments. Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary Figure 3 NgAgo has no activity to cleave linearized target or single strand target. (a) pACYCDeut-eGFP plasmid was first linearized by BamHI restriction cleavage and then co-incubated with or without the purified NgAgo preloaded with FW guide in 293T cells. NgAgo was not found to further cleave the target sequence. (b) An 86nt ssDNA coincubated with or without the purified NgAgo preloaded with guide in 293T cells at 37℃ for 8 hours. NgAgo was not found to cleave the target ssDNA. Representative figures of 3 independent experiments. Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary Figure 4 NgAgo is directed into nucleus by NLS. The engineered NLS-NgAgo was transfected to Hela cells and it shows that the expressed NLS-NgAgo was compartmented in the nucleus (DAPI+) and the cells maintained normal morphology. Scale bar = 100 μm. Representative figure of 20 independent experiments. Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary Figure 5 T7E1 assay shows the efficiency of NgAgo/gDNA system in cleaving genome. Forty-seven guides targeting 8 mammalian genome loci were tested for the cleavage efficiency of NgAgo. The percentages of indels were measured by T7E1 assay. Upper, n = 3; lower, representative figure of 3 independent experiments. Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary Figure 6 T7E1 assay using a 21nt long ssDNA guide derived from G10 to test the effects of nucleotide mismatches on the efficiency of NgAgo target cleavage. Mismatches are marked in red. Representative figure of 3 independent experiments. Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary Figure 7 A detailed structure of the donor mRFP-TGA-eGFP DNA fragment. Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary Figure 8 NgAgo has less off-target effect than Cas9 in mammalian cells. Experimental schematic of investigating off-target genome editing. gDNA and gRNA were designed targeting the same locus of the genome. A 400bp GFP gene fragment donor (GFP400) without any homologous sequence to the target was co-transfected with either NgAgo/gDNA or Cas9/gRNA. Thus, the donor could be integrated into any DSBs in the genome. Total genomic DNAs were extracted from the engineered cells and digested by endonuclease restriction enzymes Bgl II, Sal I, Sac I, Xho I, afl II and Eco47 III. Bgl II reaction generates a 6.5kb fragment containing the on-target fragment, while other fragments in unknown length are off-targets. (b) Southern blot analysis detected off-target editing by Cas9 but not by NgAgo. Representative figure of 3 independent experiments. Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary Figure 9 Full-length gel images (Unrelated lanes are marked with cross). a, for Fig 1a:Nucleic acids associated with NgAgo in E.coli. b, for Fig 1b: The in vitro plasmid cleavage assay(E.coli.-derived NgAgo). c, for Fig 1c: The in vitro plasmid cleavage assay(E.coli.-derived NgAgo, guides with or without 5' phosphorylation). d, for Fig 2a. e, for Fig 2b. f, for Fig 2c. g, for Fig 3a: The in vitro plasmid cleavage assay (293T cell-derived NgAgo). h, for Fig 3c:western blot(GFP,ACTIN). i, for Fig 3d:western blot(GFP,ACTIN). j, for Fig 4a: T7E1 (DYRK1A) . k, for Fig 4b: T7E1 (DYRK1A,EMX1,GRIN2B,GATA4,HBA2). Nature Biotechnology: doi:10.1038/nbt.3547 l, for Fig 4c: T7E1 (DYRK1A(293T,MCF-7, K562, Hela)). m, for Fig 4d: mismatches test on 24nt ssDNA guide. n, for Fig 4e: DYRK1A (NgAgo vs Cas9). o, for Fig 4f:HBA2,GATA4 (NgAgo vs Cas9). p, for Supfig 1: The in vitro plasmid cleavage assay (293T cell-derived NgAgo). q, for Supfig 2: The in vitro plasmid cleavage assay (E. Coli-derived NgAgo). r, for Supfig 3a: The in vitro linear plasmid cleavage assay. s, for Supfig 3b: The in vitro ssDNA cleavage assay. t, for Supfig 5: T7E1 (HBA2,GATA4,GRIN2B,HRES1,APOE). u, for Supfig 6: mismatches test on 21nt ssDNA guide. v, for Supplementary fig. 8: Southern blot. w, for Supplementary fig. 9: A representative experiment for NgAgo/gDNA-mediated genome editing and examination. Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary Figure 10 A representative experiment for NgAgo/gDNA-mediated genome editing and examination (T7E1 assay). (a) Schematic of experimental design shows the NgAgo/gDNA guides/target and Cas9/gRNA guides/target position, genomic PCR product and T7EI cleavage positions. Sequences of NgAgo guides: G5:5'P-CCTACCAGAATCGCCCAGTGGCTG-3' G10:5'P-CCAAAGTCCAAGGTATTAGCAGCC-3' Sequence of Cas9 guide: sg-DYRK1A: 5'-TAGCAGCCACTGGGCGATTC-3' Genomic PCR primers: DY 001 F:5’-GAAGCTCCTACACAGGTCACTG-3’ DY 705 R :5’-TTGCCCTCTTGTAGCGGTT-3’ (b) T7EI results for NgAgo/gDNA(G5 and G10) and Cas9/gRNA(sg-DYRK1A). Nature Biotechnology: doi:10.1038/nbt.3547 Index of combined PDF Supplementary Data: supplementary Note 1: A general protocol of NgAgo/gDNA-mediated genome editing and examination (T7E1 assay). Supplementary tables. A general protocol of NgAgo/gDNA-mediated genome editing and examination (T7E1 assay) 1. Cell culture 293T cells are maintained in high-glucose DMEM (HyClone) supplemented with 10% FBS (HyClone) and penicillin/streptomycin at 37°C with 5% CO2 incubation. Cells are seeded to 24-well plate (Costar) with 60% confluence 8 hours before transfection. Thirty minutes before transfection, cells are washed twice with PBS and medium is changed to high-glucose DMEM medium containing 2% FBS. 2. Transfection 2-1 NLS-NgAgo expressing plasmid is extracted with Wizard® Plus SV Minipreps DNA Purification System (Promega), and is adjusted to 100 ng/μl in 0.5x TE buffer (5 mM Tris-HCl, 0.5 mM EDTA,pH 8.0). 2-2 5’-phosphorylated ssDNA guides are dissolved to 100 ng/μl in 0.5x TE buffer (PH 8.0). For each well of a 24-well plate, 200-250 ng NLS-NgAgo plasmid and 100-300 ng guides are diluted in 50 μl Opti-MEM (Gibco); 1.25 μl lipofectamine 2000 is diluted in 50 μl Opti-MEM. Incubate the DNA mix and lipofectamine mix for 5 min. 2-3 Combine the DNA mix and lipofectamine mix with gentle pipetting and incubate for 20 min. The DNA/lipo mixture is then added into each well of cells. *Since NgAgo follows “one-guide faithful” rule, i.e. guide can only be loaded when NgAgo protein is in the process of expression, to improve the efficiency of gDNA loading to NgAgo, multiple transfection of gDNA can be conducted (e.g., 24 hours after the primary transfection) 1 Nature Biotechnology: doi:10.1038/nbt.3547 *As stated below, cells will be harvested 48-60 hours after transfection. 90% confluence of the cells on harvesting is ideal. Cell overplating significantly weakens the efficacy of genome editing. Taking HDR as an example, it occurs only during S and G2 phases. 3. Genomic DNA extraction 3-1 48-60 hours after transfection, cells are harvested by trypsin digestion. Four wells of cells are combined into a 1.5 ml EP tube. 3-2 For genomic DNA extraction, 500 μl of cell lysate buffer (50 mM Tris,100 mM EDTA,0.5% SDS,pH 8) and 10 μl proteinase K (10 mg/ml)are added into each tube and mixed gently and sufficiently. Bathe the tubes at 55℃ for 2 hours. 3-3 200 μl Tris-Phenol and 200 ul trichloromethane are added into each tube and mixed gently and sufficiently. After incubation for 5 min, samples are spun at 12,000 rpm for 15 min to separate aqueous phase from Phenol phase. 3-4 Carefully collect the aqueous phase into a clean EP tube. 3-5 Repeat the Steps 3-3 and 3-4 once and pool the aqueous phase. 3-6 Add 500 μl trichloromethane into the collected aqueous phase, mix gently and sufficiently, stay for 5 min, and then spin the sample at 12,000 rpm for 15 min to separate aqueous phase from Phenol phase. Carefully remove the aqueous phase into a clean EP tube. 3-7 Repeat the Steps 3-6 once. 3-8 Add 900 μl EtOH to the collected aqueous phase and incubate at -20°C for 30 min. 3-9 Centrifuge the sample at 12,000 rpm for 10 min, and then the DNA sediment is washed with 500 μl 75% EtOH thrice. 3-10 Air-dry the DNA sediment, add 50 μl 0.5 x TE and then adjust the genome DNA to 100 ng/μl for later use. 4. PCR Amplification (a brief example) 4-1 For 20 ul reaction system: Genomic DNA 1 μl Primer 1: (10 umol/ μl) 0.5 μl Primer 2: (10 umol/ μl) 0.5 μl 2 Nature Biotechnology: doi:10.1038/nbt.3547 2 x Taq PCR starmix with loading dye(GenStar) 10 μl H2O 8 μl 4-2 PCR program: 96℃ 3min 94℃ 30s 57℃ 30s 72℃ 20s 30 cycles 72℃ 5min 5. T7EI reaction 5-1 PCR products are purified with a PCR purification kit. 5-2 Annealing: PCR products 150 ng, 10 x NEBuffer2 1 μl, with ddH2O to a final volume of 9.6 μl. 95℃ 5 min 95~85℃ -2°C/second 85~25℃ -0.1°C/second 4℃ 1 hour 5-3 Mix the annealing product 9.6 μl with T7EI 0.4 μl and incubated the mixture at 37℃ for 30 min. 6. PAGE analysis 6-1 Equipment: Bio-Rad Mini-PROTEAN, 1 mm plate and comb. 6-2 PAGE gel preparation: 30% Arc-Bis(19:1) solution with 4M Urea 1 ml 5 x TBE 1.5 ml ddH2O 4 ml 10% APS 85 μl TEMED 3.8 μl 6-3 Run pre-electrophoresis at 140v for 30 min. 3 Nature Biotechnology: doi:10.1038/nbt.3547 6-4 Mix the 10 μl T7EI reaction product with 2 μl 6x loding buffer (Biolab) and ran electrophoresis at 140v for 30min. 7. Silver staining 7-1 Peel the Gel off from the plate and directly put it into Fix solution. Shake gently for 30 min. 7-2 Wash with Ultra-pure MiliQ water for 4 min each time thrice in dish. 7-3 Add ice-chilled staining solution and shake slowly for 25 min. 7-4 Wash with MiliQ water thrice (10 seconds each time). 7-5 Add ice-chilled developing solution and shake slowly till bands appear clearly. 7-6 Decant the developing solution and then add Fix solution to terminate reaction. *Fix solution:10% acetic acid in MiliQ water Staining solution:0.1 g Silver nitrate and 150 μl formaldehyde into 100 ml MiliQ water. Developing solution:6 g sodium carbonate, 300 μl formaldehyde and 13 μl 30% sodium thiosulfate into 200 ml MiliQ water. 8. A representative experiment (Supplementary fig. 9.) 4 Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary tables Supplementary Table 1, Guides used in this study Guide Sequence Gene FWG 5'P-TGCTTCAGCCGCTACCCCGACCAC-3' GFP RVG 5'P-GTGGTCGGGGTAGCGGCTGAAGCA-3' GFP NCG 5'P-CCGCCCCGAGTTCAAGGTGGAGCG-3' random G1 5'P-CGGTAAACTGCCCACTTGGCAGTA-3' CMV G2 5'P-CCAAGTAGGAAAGTCCCATAAGGT-3' CMV G3 5'P-AAGGGCGAGGAGCTGTTCACCGGG-3' GFP G4 5'P-GTGGTCGGGGTAGCGGCTGAAGCA-3' GFP G5 5'P-CCTACCAGAATCGCCCAGTGGCTG-3' DYRK1A G6 5'P-CAGCCACTGGGCGATTCTGGTAGG-3' DYRK1A G7 5'P-ATCGCCCAGTGGCTGCTAATACCT-3' DYRK1A G8 5'P-AGGTATTAGCAGCCACTGGGCGAT-3' DYRK1A G9 5'P-GGCTGCTAATACCTTGGACTTTGG-3' DYRK1A G10 5'P-CCAAAGTCCAAGGTATTAGCAGCC-3' DYRK1A G11 5'P-ATACCTTGGACTTTGGACAGAATG-3' DYRK1A G12 5'P-CATTCTGTCCAAAGTCCAAGGTAT-3' DYRK1A G13 5'P-GCTCCATTCTGTCCAAAGTCCAAG-3' DYRK1A G14 5'P-AGACGGTCAAATTAACGTCCATAG-3' DYRK1A G15 5'P-CTGCTCCTCTTGGTTGGTCAGGCA-3' DYRK1A G16 5'P-TGCCTGACCAACCAAGAGGAGCAG-3' DYRK1A G17 5'P-CTCCTCTTGGTTGGTCAGGCACTG-3' DYRK1A G18 5'P-CAGTGCCTGACCAACCAAGAGGAG-3' DYRK1A G19 5'P-CGCTGTCCACCTTCCAGCAGATGT-3' ACTIN G20 5'P-ACATCTGCTGGAAGGTGGACAGCG-3' ACTIN G21 5'P-CAGCAAGCAGGAGTATGACGAGTC-3' ACTIN G22 5'P-GACTCGTCATACTCCTGCTTGCTG-3' ACTIN G23 5'P-GTCCGGCCCCTCCATCGTCCACCG-3' ACTIN G24 5'P-CGGTGGACGATGGAGGGGCCGGAC-3' ACTIN 5 Nature Biotechnology: doi:10.1038/nbt.3547 G25 5'P-CCCTCCATCGTCCACCGCAAATGC-3' ACTIN G26 5'P-AGCATTTGCGGTGGACGATGGAGG-3' ACTIN G27 5'P-CCCACGAGGGCAGAGTGCTGCTTG-3' EMX1 G28 5'P-CAAGCAGCACTCTGCCCTCGTGGG-3' EMX1 G29 5'P-GCCAATGGGGAGGACATCGATGTC-3' EMX1 G30 5'P-GACATCGATGTCCTCCCCATTGGC-3' EMX1 G31 5'P-TGTCACCTCCAATGACTAGGGTGG-3' EMX1 G32 5'P-CCACCCTAGTCATTGGAGGTGACA-3' EMX1 G33 5'P-GCAACCACAAACCCACGAGGGCAG-3' EMX1 G34 5'P-CTGCCCTCGTGGGTTTGTGGTTGC-3' EMX1 G35 5'P-TGCTGGCCAGGCCCCTGCGTGGGC-3' EMX1 G36 5'P-GCCCACGCAGGGGCCTGGCCAGCA-3' EMX1 G37 5'P-GAGATGGCGCCTTCCTCTCAGGGC-3' HBA2 G38 5'P-GCGCCTTCCTCTCAGGGCAGAGGA-3' HBA2 G39 5'P-CTCTTCTCTGCACAGCTCCTAAGC-3' HBA2 G40 5'P-GGCGCCCGCGCCGTGCATGAAGGC-3' GATA4 G41 5'P-AGCTCCGGTGGGGCCGCGTCTGGT-3' GATA4 G42 5'P-GGTCCCTGGCGGCCGCCGCCGCCG-3' GATA4 G43 5'P-GATAAGGTCCTTGAATTGCAGTAT-3' GRIN2B G44 5'P-TTGCAGGGAGTCGACGAGTTGAAG-3' GRIN2B G45 5'P-ATGAATGAGACCGACCCAAAGAGC-3' GRIN2B G46 5'P-GCGGGGCCGGGCCTGGGCTGCGGG-3' HRES1 G47 5'P-ACCGTAGGTTTCGGACATGGCCGT-3' HRES1 G48 5'P-CTCCACCCTCCGTCCGGCCGCGAC-3' HRES1 G49 5'P-CGCGTGCGGGCCGCCACTGTGGGC-3' APOE G50 5'P-CATGGCCTGCACCTCGCCGCGGTA-3' APOE G51 5'P-GCCTCAAGAGCTGGTTCGAGCCCC-3' APOE G52 5'P-AGAAGGTATACACGTCGGAAGAAT-3' target 6 Nature Biotechnology: doi:10.1038/nbt.3547 Supplementary table 2, Primers used in the T7E1 assay Primer Sequence DYRK1A test F 5’-GTTCTTTCAGGTGCGTCA-3' DYRK1A test R 5’-GGGACTCTTCTCTATCAGCC-3' HBA2 test F 5’-ACGGCTCTGCCCAGGTTA-3' HBA2 test R 5’-CATTGTTGGCACATTCCG-3' GATA4 test F 5’-CCCCTTTGATTTTTGATCTTCG-3' GATA4 test R 5’-TGTGCAGGACCGGGCTGT-3' GRIN2B test F 5’-CAGGAGGGCCAGGAGATTTG-3' GRIN2B test R 5’-TGAAATCGAGGATCTGGGCG-3' EMX1 test F 5’-CCATCCCCTTCTGTGAATGT-3' EMX1 test R 5’-GGAGATTGGAGACACGGAGA-3' APOE test F 5’-GGAACTGGAGGAACAACTGAC-3' APOE test R 5’-TCGGCGTTCAGTGATTGT-3' HRES1 test F 5’-ATGCGCTGTGCACAGCGC-3' HRES1 test R 5’-TCAGGGAAATCGGGACTCAGC-3' β-ACTIN test F 5’-CACGAAACTACCTTCAACTCC-3' β-ACTIN test R 5’-GACTTCCTGTAACAACGCATC-3' 7 Nature Biotechnology: doi:10.1038/nbt.3547 Length 584BP 577BP 705BP 696BP 639BP 680BP 676BP 700BP Supplementary table 3, Oligos, plasmids and constructs used in this study plasmid oligos NgAgo-6 P-1 F NgAgo-6P-1 NgAgo-6 P-1 R FLAG Hid Ⅲ F FLAG-NgAgo-HA -pcDNA3.1 HA Bamh ⅠR NLS-NgA go F1 NgAgo-N LS-Hind Ⅲ F2 NLS-NgAgo-red NgAgo-B am R NLS-NgAgo-pcD NA3.1 NgAgo-N LS-Hind Ⅲ F2 NgAgo-B am-TGAR SpCas9Hind - F SpCas9-pcDNA3 .1 SpCas9Bam-R pACY600 -Hind F pACY268 3-Bam R GFP-Hin d R pACYCDuet-GFP CMV-Bam F sequence 5’-GAAGATCTACA GTGATTGACCTCGA TTCG-3’ 5’-CCGCTCGAGCT AGAGGAATCCGACA TTAGACTCG-3’ 5’-CCCAAGCTTGC CACCATGGATTACA AGGATGACGACGAT AAGACAGTGATTGA CCTCGATTCG-3’ 5’-CGGGATCCTTA AGCGTAATCTGGAA CATCGTATGGGTAG AGGAATCCGACATT AGACTCG-3’ 5’-CCAAAAAAGAA GAGAAAGGTAGCCA CAGTGATTGACCTC GATTCG-3’ 5’-CCCAAGCTTGC CACCATGGTGCCAA AAAAGAAGAGAAAG GTAGCC-3’ 5’-CGGGATCCCGG AGGAATCCGACATT AGACTCG-3’ 5’-CCCAAGCTTGC CACCATGGTGCCAA AAAAGAAGAGAAAG GTAGCC-3’ 5’-CGGGATCCtca GAGGAATCCGACAT TAGACTCG-3’ 5’-CCCAAGCTTGC CACCATGGACTATA AGGACCACGACG-3 ’ 5’-CGGGATCCTCA CTTTTTCTTTTTTG CCTGGC-3’ 5’-CCCAAGCTTAA CGACCCTGCCCTGA AC-3’ 5’-CGCGGATCCGG GCATGACTAACATG AGAATTAC-3’ 5’-CCCAAGCTTGG GGGACTTGTACAGC TCGTCC-3’ 5’-CGCGGATCCTA GTTATTAATAGTAA TCAATTACG-3’ 8 Nature Biotechnology: doi:10.1038/nbt.3547 template backbone restrictio n sites genomic DNA of Natronobact eriumgregor yi SP2 pGEX6P-1 BamhI,Bgl Ⅱand XhoI genomic DNA of Natronobact eriumgregor yi SP2 pcDNA3.1 /Hygro(+ ) HindⅢ and BamhI genomic DNA of Natronobact eriumgregor yi SP2 pDsRed MonomerN1 HindⅢ and BamhI NLS-NgAgo-r ed pcDNA3.1 /Hygro(+ ) HindⅢ and BamhI pX330-U6-Ch imeric_BB-C Bh-hSpCas9 pcDNA3.1 /Hygro(+ ) HindⅢ and BamhI pACYCDuet-1 EGFP-N1 without MCS BamhI and HindⅢ sgRNA F sgRNA(DYRK1A) sgRNA R sgRNA1 F sgRNA(CMV) sgRNA1 R sgRNA2 F sgRNA(GFP) sgRNA2 R sgRNA3 F sgRNA(HBA2) sgRNA3 R sgRNA4 F sgRNA(GATA4) sgRNA4 R 5’-CACCGGCCCAG TGGCTGCTAATACC T-3’ 5’-AAACAGGTATT AGCAGCCACTGGGC C-3’ 5’-CACCGGCTGGG CATAATGCCAGGCG G-3’ 5’-AAACCCGCCTG GCATTATGCCCAGC C-3’ 5’-CACCGGCTCGT GACCACCCTGACCT A-3’ 5’-AAACTAGGTCA GGGTGGTCACGAGC C-3’ 5’-CACCGGGAGAT GGCGCCTTCCTCTC A-3’ 5’-AAACTGAGAGG AAGGCGCCATCTCC C-3’ 5’-CACCGGGGCGC CCGCGCCGTGCATG A-3’ 5’-AAACTCATGCA CGGCGCGGGCGCCC C-3’ 9 Nature Biotechnology: doi:10.1038/nbt.3547 phU6-gRN A BbvII phU6-gRN A BbvII phU6-gRN A BbvII phU6-gRN A BbvII phU6-gRN A BbvII
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