M of the gel indicate mutation percentages calculated by band intensities. (C) DNA sequences of the wild-type (WT) and mutant clones, with ZFN recognition sites underlined. Dashes indicate deleted bases, and small bold letters indicate inserted bases. The number of occurrences is shown in parentheses; X1 indicates that each clone was detected once. Mutation frequencies were calculated by dividing the number of mutant clones by the number of total clones. doi:10.1371/journal.pone.0056476.g(hygromycin reporter). Huh 7.5 cells were electroporated using a 100-ml tip at voltage 1, 100 V, width 30 ms, and one pulse in the Neon Transfection System (Invitrogen) with a total of 8 mg plasmid DNA (1:1:2 weight ratio).T7E1 assayThe T7E1 assay was performed as previously described [3,23]. Briefly, Title Loaded From File genomic DNA was isolated using the DNeasy Blood Tissue Kit (Qiagen) according to the manufacturer’s instructions. The region of DNA containing the nuclease target site was PCRamplified using the primers previously described [3]. The amplicons were denatured by heating and annealed to form heteroduplex DNA, which was treated with 5 units of T7 endonuclease 1 (New England Biolabs) for 15 to 20 min at 37uC and then analyzed by 2 agarose gel electrophoresis.Title Loaded From File magnetic separationThe transfected cells were cultured for one day at 37uC followed by culture at 30uC (cold shock) [24] for two days and subjected to magnetic separation. Trypsinized cell suspensions were mixed with magnetic bead-conjugated antibody against H-2Kk (MACSelect Kk microbeads; Miltenyi Biotech, Germany) and incubated for 20 min at 4uC. Labeled cells were separated using a column (MACS LS column; Miltenyi Biotech) according to the manufacturer’s instructions.Sequencing analysisPCR amplicons that included ZFN-target sites were purified using the Gel Extraction Kit (MACHERRY-NALGEN) and cloned into the T-Blunt vector using the T-Blunt PCR Cloning Kit (SolGent). Cloned plasmids were sequenced using the primers used for PCR amplification.Hygromycin selectionTwo days after transfection, hygromycin selection was performed by culturing the cells in the presence of 2 mg/ml of hygromycin B for two days at 37uC. For clonal analysis, hygromycin-selected cells were plated at a density of 3,000 cells/ 100 mm dish, and the clonal colonies were manually picked 10 days after plating.Results and Discussion Enrichment of mutant cells using magnetic reportersWe first devised reporters that express mRFP, eGFP, and a truncated H-2Kk surface marker (H-2Kk). To allow measurementFlow Cytometer-Free Enrichment of Mutant CellsFigure 3. Surrogate reporter-mediated magnetic separations enrich ZFN- and TALEN-driven mutant cells. Nuclease-driven mutations were detected by the T7E1 assay. Arrows indicate the expected positions of DNA bands cleaved by mismatch-sensitive T7E1. The numbers at the bottom of the gels indicate mutation percentages calculated by band intensities. doi:10.1371/journal.pone.0056476.gof the activity of engineered nucleases, we inserted the nuclease target sequence between the sequences encoding mRFP and H2Kk (Figure 1). To prevent the expression of H-2Kk and GFP in the absence of the engineered nuclease activity, we prepared double barriers: we made sequences encoding GFP and H-2Kk out of frame and also placed a stop codon before GFP and H-2Kk. When target sequences in the reporter plasmids are cleaved by the engineered nucleases and indels are generated via mutagenic nonhomologous end-joining, the f.M of the gel indicate mutation percentages calculated by band intensities. (C) DNA sequences of the wild-type (WT) and mutant clones, with ZFN recognition sites underlined. Dashes indicate deleted bases, and small bold letters indicate inserted bases. The number of occurrences is shown in parentheses; X1 indicates that each clone was detected once. Mutation frequencies were calculated by dividing the number of mutant clones by the number of total clones. doi:10.1371/journal.pone.0056476.g(hygromycin reporter). Huh 7.5 cells were electroporated using a 100-ml tip at voltage 1, 100 V, width 30 ms, and one pulse in the Neon Transfection System (Invitrogen) with a total of 8 mg plasmid DNA (1:1:2 weight ratio).T7E1 assayThe T7E1 assay was performed as previously described [3,23]. Briefly, genomic DNA was isolated using the DNeasy Blood Tissue Kit (Qiagen) according to the manufacturer’s instructions. The region of DNA containing the nuclease target site was PCRamplified using the primers previously described [3]. The amplicons were denatured by heating and annealed to form heteroduplex DNA, which was treated with 5 units of T7 endonuclease 1 (New England Biolabs) for 15 to 20 min at 37uC and then analyzed by 2 agarose gel electrophoresis.Magnetic separationThe transfected cells were cultured for one day at 37uC followed by culture at 30uC (cold shock) [24] for two days and subjected to magnetic separation. Trypsinized cell suspensions were mixed with magnetic bead-conjugated antibody against H-2Kk (MACSelect Kk microbeads; Miltenyi Biotech, Germany) and incubated for 20 min at 4uC. Labeled cells were separated using a column (MACS LS column; Miltenyi Biotech) according to the manufacturer’s instructions.Sequencing analysisPCR amplicons that included ZFN-target sites were purified using the Gel Extraction Kit (MACHERRY-NALGEN) and cloned into the T-Blunt vector using the T-Blunt PCR Cloning Kit (SolGent). Cloned plasmids were sequenced using the primers used for PCR amplification.Hygromycin selectionTwo days after transfection, hygromycin selection was performed by culturing the cells in the presence of 2 mg/ml of hygromycin B for two days at 37uC. For clonal analysis, hygromycin-selected cells were plated at a density of 3,000 cells/ 100 mm dish, and the clonal colonies were manually picked 10 days after plating.Results and Discussion Enrichment of mutant cells using magnetic reportersWe first devised reporters that express mRFP, eGFP, and a truncated H-2Kk surface marker (H-2Kk). To allow measurementFlow Cytometer-Free Enrichment of Mutant CellsFigure 3. Surrogate reporter-mediated magnetic separations enrich ZFN- and TALEN-driven mutant cells. Nuclease-driven mutations were detected by the T7E1 assay. Arrows indicate the expected positions of DNA bands cleaved by mismatch-sensitive T7E1. The numbers at the bottom of the gels indicate mutation percentages calculated by band intensities. doi:10.1371/journal.pone.0056476.gof the activity of engineered nucleases, we inserted the nuclease target sequence between the sequences encoding mRFP and H2Kk (Figure 1). To prevent the expression of H-2Kk and GFP in the absence of the engineered nuclease activity, we prepared double barriers: we made sequences encoding GFP and H-2Kk out of frame and also placed a stop codon before GFP and H-2Kk. When target sequences in the reporter plasmids are cleaved by the engineered nucleases and indels are generated via mutagenic nonhomologous end-joining, the f.
