zr plasmid miniprep kit  (Zymo Research)


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    Name:
    Zymoprep Yeast Plasmid Miniprep II
    Description:
    The Zymoprep Yeast Plasmid Miniprep II is a simple and efficient yeast plasmid miniprep that is based on the E. coli alkaline lysis method but using Zymolyase as the first solution. The kit provides all the necessary reagents for plasmid isolation from S. cerevisiae, C. albicans and S. pombe, and any fungi whose cell walls are susceptible to yeast lytic enzyme lysis. The procedure is simple and efficient, and there is no need for glass beads or phenol. The Zymoprep II recovers about 5 fold more plasmid DNA compared to Zymoprep I and eliminates the isopropanol precipitation step. Reliably recover plasmid DNA from yeast colonies, patches on plates, or as liquid cultures. The system is ideal for low-copy number and hard to isolate plasmids. Eluted plasmid DNA can be used directly for E. Coli transformation, PCR, and Southern blot analysis.
    Catalog Number:
    D2004
    Price:
    None
    Applications:
    Yeast Plasmid Purification
    Size:
    50 units
    Category:
    Life Science Reagents and Media
    Score:
    85
    Buy from Supplier


    Structured Review

    Zymo Research zr plasmid miniprep kit
    Zymoprep Yeast Plasmid Miniprep II
    The Zymoprep Yeast Plasmid Miniprep II is a simple and efficient yeast plasmid miniprep that is based on the E. coli alkaline lysis method but using Zymolyase as the first solution. The kit provides all the necessary reagents for plasmid isolation from S. cerevisiae, C. albicans and S. pombe, and any fungi whose cell walls are susceptible to yeast lytic enzyme lysis. The procedure is simple and efficient, and there is no need for glass beads or phenol. The Zymoprep II recovers about 5 fold more plasmid DNA compared to Zymoprep I and eliminates the isopropanol precipitation step. Reliably recover plasmid DNA from yeast colonies, patches on plates, or as liquid cultures. The system is ideal for low-copy number and hard to isolate plasmids. Eluted plasmid DNA can be used directly for E. Coli transformation, PCR, and Southern blot analysis.
    https://www.bioz.com/result/zr plasmid miniprep kit/product/Zymo Research
    Average 99 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    zr plasmid miniprep kit - by Bioz Stars, 2019-12
    99/100 stars

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    Related Articles

    Clone Assay:

    Article Title: Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen
    Article Snippet: DNA purification from yeast was performed using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research). .. DNA purification from yeast was performed using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research). .. Plasmids were amplified in E. coli DH10β and sequenced.

    Article Title: Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast
    Article Snippet: Paragraph title: Gene cloning and plasmid construction ... Plasmid DNA was isolated from positive transformants using a Zymoprep™ Yeast Plasmid Miniprep II Kit (Zymo Research) and used to transform NEB 5-alpha Electrocompetent E. coli (New England Biolabs) by electroporation.

    Article Title: Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding
    Article Snippet: Four iterative rounds of enrichment were performed. .. Plasmid DNA from the enriched library was recovered using a Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) following manufacturer’s protocol, transformed into bacteria, and individual clones were sequenced by standard Sanger DNA sequencing methods. .. Plasmid DNA was subsequently mutated by error-prone PCR of either the entire Fn3 gene or the paratope loops using nucleotide analogues, 8-oxo-2’-deoxyguanosine-5’-triphosphate (8-oxo-dGTP) (TriLink Biotechnologies) and 2’deoxy-p-nucleoside-5’-triphosphate (dPTP) (TriLink Biotechnologies) [ ].

    Article Title: Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach
    Article Snippet: Paragraph title: Cloning procedures. ... Y. lipolytica minipreps were performed by using a Zymoprep yeast plasmid miniprep II kit (Zymo Research Corporation).

    Article Title: Cloning of the Repertoire of Individual Plasmodium falciparum var Genes Using Transformation Associated Recombination (TAR)
    Article Snippet: All yeast TAR clones were propagated on selective medium and yeast genomic DNA was isolated by phenol/chloroform purification (as described in ) with subsequent precipitation. .. Alternatively, yeast plasmid DNA was directly purified using the Zymoprep II™ Yeast Plasmid Miniprep Kit (Zymo Research) or the QIAprep Spin Miniprep Kit (Qiagen).

    Article Title: AhR/Arnt:XRE interaction: Turning false negatives into true positives in the modified yeast one-hybrid assay
    Article Snippet: Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA). .. Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA).

    Article Title: Construction and engineering of large biochemical pathways via DNA assembler
    Article Snippet: Paragraph title: 2.3. Verification of the clones ... Zymoprep II yeast plasmid miniprep (Zymo Research, Orange, CA, USA).

    Amplification:

    Article Title: Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide
    Article Snippet: Aga2-VH fusions were subcloned from existing pET-17b constructs using PCR amplification to introduce overhangs complementary to the pCTCON2 yeast display plasmid. .. Overnight yeast cell cultures were miniprepped (D2004, Zymoprep II yeast miniprep kit, Zymo Research) and subsequently transformed into electroporation competent XL1-blue bacterial cells (200228, Agilent Technologies).

    Article Title: Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast
    Article Snippet: Individual exons of the STS genes were amplified by PCR with 35–40 bp overhangs that overlap with neighbouring exons or plasmid backbone and stitched together to form the respective ‘intronless’ cDNA genes by yeast-mediated in vivo DNA recombination. .. Plasmid DNA was isolated from positive transformants using a Zymoprep™ Yeast Plasmid Miniprep II Kit (Zymo Research) and used to transform NEB 5-alpha Electrocompetent E. coli (New England Biolabs) by electroporation.

    Article Title: A tetO toolkit to alter expression of genes in Saccharomyces cerevisiae
    Article Snippet: Sanger sequence and analysis was performed as previously described . .. Deep sequencing of plasmid DNA was performed on an Illumina Miseq by purifying DNA using the Zymoprep yeast plasmid prep II (Zymo Research), and PCR amplification for 12 cycles. .. The endogenous promoter of HIS3 was replaced from -1 to -122 bp upstream from the start codon with a single tetO site derived from the previously published construct pCM188 .

    Article Title: Identification of Ci
    Article Snippet: The 5′- or 3′-UTRs of mutant replicons were amplified from the colonies, and their sequences were verified (MC Lab, South San Francisco, CA). .. Plasmid DNAs harboring the mutations were recovered using the Zymoprep II yeast plasmid minipreparation kit (Zymo Research), and 2 μl were used to transform 20 μl of MAX Efficiency Stbl2-competent cells (Invitrogen).

    Article Title: Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus
    Article Snippet: Yeast propagation was performed in the presence of 2% raffinose + 0.1% glucose at 30°C for at least 12 h prior to induction. .. Plasmids were isolated from yeast populations using the Zymoprep-II kit (Zymo Research) and transformed into Escherichia coli DH5α by heat shock for amplification and/or sequencing. .. Sequencing was performed on 40–60 clones for a given selection output.

    Cytometry:

    Article Title: Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis
    Article Snippet: After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies). .. After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies).

    Construct:

    Article Title: Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide
    Article Snippet: Aga2-VH fusions were subcloned from existing pET-17b constructs using PCR amplification to introduce overhangs complementary to the pCTCON2 yeast display plasmid. .. Overnight yeast cell cultures were miniprepped (D2004, Zymoprep II yeast miniprep kit, Zymo Research) and subsequently transformed into electroporation competent XL1-blue bacterial cells (200228, Agilent Technologies).

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: By using different amounts of template DNA, 2 libraries differing in their mutation rates were constructed. .. After growing the S. cerevisiae -libraries in SD-CAA-medium [20 g/l glucose, 0.1 M KH2 PO4 /K2 HPO4 , pH 6, 10 g/l (NH4 )2 SO4 , 0.1 g/l l -leucine (all from Sigma, St. Louis, MO), 3.4 g/l yeast nitrogen base, 10 g/l bacto casamino acids (both from Difco, BD, Franklin Lakes, NJ)] at 28 °C for 48 h, pYD1 plasmid DNA was isolated by using the Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research, Orange, CA) and transformed into Escherichia coli Top 10 for sequencing.

    Incubation:

    Article Title: Efficient proximity labeling in living cells and organisms with TurboID
    Article Snippet: For negative selections , gates were drawn to collect yeast with AF647 signal and no PE signal above background ( ). .. After sorting, yeast were collected in SDCAA medium containing 1% penicillin-streptomycin and incubated at 30°C for 24 h. 1 mL of the growing culture was removed for DNA extraction using the Zymoprep yeast Plasmid Miniprep II (Zymo Research) kit according to manufacturer protocols (using 6 μL zymolyase, vigorously vortex after lysis), and at least ten-fold excess of the number of cells retained during sorting were propagated in SDCAA + 1% pen-strep to ensure oversampling (yeast cells were passaged in this manner at least two times prior to the next round of selection). .. To analyze yeast populations and clones by FACS ( ; ), yeast samples were prepared on a small scale (1 mL cultures) as described above, and analyzed on a BD Accuri flow cytometer (BD Biosciences).

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: After washing with PBSF, cells were incubated with 5 μg/ml SA-633 and 5 μg/ml GaC-488 at 4°C for 30 min. After washing, cells were resuspended in PBSF buffer and sorted using FACS Aria (BD Bioscience). .. After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    Article Title: Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding
    Article Snippet: Cells were washed and incubated with a goat anti-chicken Alexa Fluor 647 (AF647) conjugate (Thermo Fisher #A-21449, 1:250) and either Alexa Fluor 488 (AF488)-conjugated streptavidin (Thermo Fisher #S11223, 1:700) to detect the biotin molecules of the biotinylated Fc-tagged MSLN, or a goat anti-human IgG Fc FITC conjugate (Thermo Fisher #A18830, 1:500) to detect the human Fc domain of the biotinylated Fc-tagged MSLN. .. Plasmid DNA from the enriched library was recovered using a Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) following manufacturer’s protocol, transformed into bacteria, and individual clones were sequenced by standard Sanger DNA sequencing methods.

    Activity Assay:

    Article Title: Efficient proximity labeling in living cells and organisms with TurboID
    Article Snippet: From population P3, gates were drawn to collect yeast with the highest activity/expression ratio, i.e., positive for AF647 signal that also had high PE signal ( ). .. After sorting, yeast were collected in SDCAA medium containing 1% penicillin-streptomycin and incubated at 30°C for 24 h. 1 mL of the growing culture was removed for DNA extraction using the Zymoprep yeast Plasmid Miniprep II (Zymo Research) kit according to manufacturer protocols (using 6 μL zymolyase, vigorously vortex after lysis), and at least ten-fold excess of the number of cells retained during sorting were propagated in SDCAA + 1% pen-strep to ensure oversampling (yeast cells were passaged in this manner at least two times prior to the next round of selection).

    Cell Culture:

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research). .. Plasmids encoding the 5 unique antibody clones above were re-transformed into strain EBY100.

    Article Title: Improving Saccharomyces cerevisiae ethanol production and tolerance via RNA polymerase II subunit Rpb7
    Article Snippet: After three to five successive subcultures, the enriched cell culture diluted by 106 –107 was spread onto YPAD plates. .. Individual colonies were randomly picked for miniprep [Zymoprep II kit (Zymo Research, Orange, CA, USA)] and sent for DNA sequencing.

    Expressing:

    Article Title: Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis
    Article Snippet: A 10-fold oversampling of the expanded cells was re-suspended in SGCAA media for surface display fusion expression and sorting in the next round of screening. .. After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies).

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research). .. Plasmids encoding the 5 unique antibody clones above were re-transformed into strain EBY100.

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: Directly after the CH3-domain a stop codon was introduced in order to avoid expression of any C-terminal tags that are present on the vector. .. After growing the S. cerevisiae -libraries in SD-CAA-medium [20 g/l glucose, 0.1 M KH2 PO4 /K2 HPO4 , pH 6, 10 g/l (NH4 )2 SO4 , 0.1 g/l l -leucine (all from Sigma, St. Louis, MO), 3.4 g/l yeast nitrogen base, 10 g/l bacto casamino acids (both from Difco, BD, Franklin Lakes, NJ)] at 28 °C for 48 h, pYD1 plasmid DNA was isolated by using the Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research, Orange, CA) and transformed into Escherichia coli Top 10 for sequencing.

    Transformation Assay:

    Article Title: Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide
    Article Snippet: The PCR products were mixed with pCTCON2 plasmid that was digested with NheI and SalI, and transformed into the EBY100 strain for homologous recombination and selection on SD-CAA agar plates. .. Overnight yeast cell cultures were miniprepped (D2004, Zymoprep II yeast miniprep kit, Zymo Research) and subsequently transformed into electroporation competent XL1-blue bacterial cells (200228, Agilent Technologies). .. Individual bacterial colonies were miniprepped (27106, Qiagen) and sequenced.

    Article Title: Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis
    Article Snippet: A 10-fold oversampling of the expanded cells was re-suspended in SGCAA media for surface display fusion expression and sorting in the next round of screening. .. After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies). .. Individual clones were isolated and the MBD2 gene was sequenced using the forward primer 5′-CCC CTC AAC TAG CAA AGG CAG-3′.

    Article Title: Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast
    Article Snippet: In vivo yeast recombination cloning was carried out using a Frozen-EZ Yeast Transformation II Kit™ (Zymo Research) where competent S. cerevisiae BJ5464 [ ] was transformed with the DNA fragments (PCR products) of the respective genes and linearized plasmid backbone derived from YEplac-ADH2p [ , ]. .. Plasmid DNA was isolated from positive transformants using a Zymoprep™ Yeast Plasmid Miniprep II Kit (Zymo Research) and used to transform NEB 5-alpha Electrocompetent E. coli (New England Biolabs) by electroporation.

    Article Title: Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding
    Article Snippet: Four iterative rounds of enrichment were performed. .. Plasmid DNA from the enriched library was recovered using a Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) following manufacturer’s protocol, transformed into bacteria, and individual clones were sequenced by standard Sanger DNA sequencing methods. .. Plasmid DNA was subsequently mutated by error-prone PCR of either the entire Fn3 gene or the paratope loops using nucleotide analogues, 8-oxo-2’-deoxyguanosine-5’-triphosphate (8-oxo-dGTP) (TriLink Biotechnologies) and 2’deoxy-p-nucleoside-5’-triphosphate (dPTP) (TriLink Biotechnologies) [ ].

    Article Title: Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach
    Article Snippet: Y. lipolytica minipreps were performed by using a Zymoprep yeast plasmid miniprep II kit (Zymo Research Corporation). .. The transformation of E. coli strains was performed by using standard electroporator protocols ( ).

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: The library inserts comprised homologous regions to the BamHI/NotI-digested pYD1 backbone on both sides in order to facilitate gap repair driven homologous recombination in S. cerevisiae . .. After growing the S. cerevisiae -libraries in SD-CAA-medium [20 g/l glucose, 0.1 M KH2 PO4 /K2 HPO4 , pH 6, 10 g/l (NH4 )2 SO4 , 0.1 g/l l -leucine (all from Sigma, St. Louis, MO), 3.4 g/l yeast nitrogen base, 10 g/l bacto casamino acids (both from Difco, BD, Franklin Lakes, NJ)] at 28 °C for 48 h, pYD1 plasmid DNA was isolated by using the Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research, Orange, CA) and transformed into Escherichia coli Top 10 for sequencing. .. Furthermore, cell surface expression was induced and analyzed using flow cytometry as described below.

    Article Title: AhR/Arnt:XRE interaction: Turning false negatives into true positives in the modified yeast one-hybrid assay
    Article Snippet: Paragraph title: Transformation, DNA preparation, and plasmid rescue ... Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA).

    Article Title: Identification of Ci
    Article Snippet: The linearized WT or the mutant replicon plasmid was mixed with the vacuum-dried mutant PCR fragments, and the mixture was introduced into Saccharomyces cerevisiae YPH857 (50 μl) made chemically competent using the S.c. EasyComp Transformation Kit (Invitrogen) ( ). .. Plasmid DNAs harboring the mutations were recovered using the Zymoprep II yeast plasmid minipreparation kit (Zymo Research), and 2 μl were used to transform 20 μl of MAX Efficiency Stbl2-competent cells (Invitrogen).

    Article Title: Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus
    Article Snippet: Yeast propagation was performed in the presence of 2% raffinose + 0.1% glucose at 30°C for at least 12 h prior to induction. .. Plasmids were isolated from yeast populations using the Zymoprep-II kit (Zymo Research) and transformed into Escherichia coli DH5α by heat shock for amplification and/or sequencing. .. Sequencing was performed on 40–60 clones for a given selection output.

    Derivative Assay:

    Article Title: Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast
    Article Snippet: In vivo yeast recombination cloning was carried out using a Frozen-EZ Yeast Transformation II Kit™ (Zymo Research) where competent S. cerevisiae BJ5464 [ ] was transformed with the DNA fragments (PCR products) of the respective genes and linearized plasmid backbone derived from YEplac-ADH2p [ , ]. .. Plasmid DNA was isolated from positive transformants using a Zymoprep™ Yeast Plasmid Miniprep II Kit (Zymo Research) and used to transform NEB 5-alpha Electrocompetent E. coli (New England Biolabs) by electroporation.

    Electroporation:

    Article Title: Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide
    Article Snippet: The PCR products were mixed with pCTCON2 plasmid that was digested with NheI and SalI, and transformed into the EBY100 strain for homologous recombination and selection on SD-CAA agar plates. .. Overnight yeast cell cultures were miniprepped (D2004, Zymoprep II yeast miniprep kit, Zymo Research) and subsequently transformed into electroporation competent XL1-blue bacterial cells (200228, Agilent Technologies). .. Individual bacterial colonies were miniprepped (27106, Qiagen) and sequenced.

    Article Title: Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast
    Article Snippet: Yeast transformants grown on synthetic dropout agar plate lacking uracil were screened by PCR. .. Plasmid DNA was isolated from positive transformants using a Zymoprep™ Yeast Plasmid Miniprep II Kit (Zymo Research) and used to transform NEB 5-alpha Electrocompetent E. coli (New England Biolabs) by electroporation. .. Plasmid DNA was isolated from the positive clones grown on LB-ampicillin using the alkaline lysis method and further verified by DNA sequencing.

    Flow Cytometry:

    Article Title: Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis
    Article Snippet: After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies). .. After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies).

    Article Title: Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding
    Article Snippet: Cells were washed and incubated with a goat anti-chicken Alexa Fluor 647 (AF647) conjugate (Thermo Fisher #A-21449, 1:250) and either Alexa Fluor 488 (AF488)-conjugated streptavidin (Thermo Fisher #S11223, 1:700) to detect the biotin molecules of the biotinylated Fc-tagged MSLN, or a goat anti-human IgG Fc FITC conjugate (Thermo Fisher #A18830, 1:500) to detect the human Fc domain of the biotinylated Fc-tagged MSLN. .. Plasmid DNA from the enriched library was recovered using a Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) following manufacturer’s protocol, transformed into bacteria, and individual clones were sequenced by standard Sanger DNA sequencing methods.

    Ligation:

    Article Title: Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen
    Article Snippet: Phusion DNA Polymerase, Taq polymerase, DNA restriction and ligation enzymes were purchased from New England Biolabs (NEB), and DNA purification and gel-extraction were performed using Geneaid kits. .. DNA purification from yeast was performed using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    Article Title: Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach
    Article Snippet: Ligation reactions were performed overnight at 16°C by using T4 DNA ligase (Fermentas). .. Y. lipolytica minipreps were performed by using a Zymoprep yeast plasmid miniprep II kit (Zymo Research Corporation).

    Library Screening:

    Article Title: Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis
    Article Snippet: Paragraph title: Library screening for MBD2 variants with improved binding affinity to methylated CpGs ... After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies).

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: Paragraph title: Yeast library screening ... After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    Introduce:

    Article Title: Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide
    Article Snippet: Aga2-VH fusions were subcloned from existing pET-17b constructs using PCR amplification to introduce overhangs complementary to the pCTCON2 yeast display plasmid. .. Overnight yeast cell cultures were miniprepped (D2004, Zymoprep II yeast miniprep kit, Zymo Research) and subsequently transformed into electroporation competent XL1-blue bacterial cells (200228, Agilent Technologies).

    Generated:

    Article Title: Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach
    Article Snippet: Purifications of small DNA fragments ( < 200 bp) generated during plasmid construction were performed by using the MERmaid Spin kit (Qbiogene). .. Y. lipolytica minipreps were performed by using a Zymoprep yeast plasmid miniprep II kit (Zymo Research Corporation).

    DNA Sequencing:

    Article Title: Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding
    Article Snippet: Four iterative rounds of enrichment were performed. .. Plasmid DNA from the enriched library was recovered using a Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) following manufacturer’s protocol, transformed into bacteria, and individual clones were sequenced by standard Sanger DNA sequencing methods. .. Plasmid DNA was subsequently mutated by error-prone PCR of either the entire Fn3 gene or the paratope loops using nucleotide analogues, 8-oxo-2’-deoxyguanosine-5’-triphosphate (8-oxo-dGTP) (TriLink Biotechnologies) and 2’deoxy-p-nucleoside-5’-triphosphate (dPTP) (TriLink Biotechnologies) [ ].

    Article Title: A tetO toolkit to alter expression of genes in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: Oligonucleotides and DNA sequencing ... Deep sequencing of plasmid DNA was performed on an Illumina Miseq by purifying DNA using the Zymoprep yeast plasmid prep II (Zymo Research), and PCR amplification for 12 cycles.

    Article Title: Improving Saccharomyces cerevisiae ethanol production and tolerance via RNA polymerase II subunit Rpb7
    Article Snippet: After three to five successive subcultures, the enriched cell culture diluted by 106 –107 was spread onto YPAD plates. .. Individual colonies were randomly picked for miniprep [Zymoprep II kit (Zymo Research, Orange, CA, USA)] and sent for DNA sequencing. .. To eliminate the possibilities of introducing mutations from plasmid backbone and host strain during enrichment selection, mutant RPB7 gene fragment was digested and re-inserted into a fresh plasmid p41K-RPB7 backbone and retransformed into fresh BY4742 background, generating mutant M1 used in this study.

    Sequencing:

    Article Title: In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity
    Article Snippet: Paragraph title: Sequencing library preparation ... Plasmid was extracted from at least 107 yeast cells per sample using Zymoprep Yeast Plasmid Miniprep II (Zymo Research, Irvine, CA) according to the manufacturer's instructions.

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: The library inserts comprised homologous regions to the BamHI/NotI-digested pYD1 backbone on both sides in order to facilitate gap repair driven homologous recombination in S. cerevisiae . .. After growing the S. cerevisiae -libraries in SD-CAA-medium [20 g/l glucose, 0.1 M KH2 PO4 /K2 HPO4 , pH 6, 10 g/l (NH4 )2 SO4 , 0.1 g/l l -leucine (all from Sigma, St. Louis, MO), 3.4 g/l yeast nitrogen base, 10 g/l bacto casamino acids (both from Difco, BD, Franklin Lakes, NJ)] at 28 °C for 48 h, pYD1 plasmid DNA was isolated by using the Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research, Orange, CA) and transformed into Escherichia coli Top 10 for sequencing. .. Furthermore, cell surface expression was induced and analyzed using flow cytometry as described below.

    Article Title: A tetO toolkit to alter expression of genes in Saccharomyces cerevisiae
    Article Snippet: Sanger sequence and analysis was performed as previously described . .. Deep sequencing of plasmid DNA was performed on an Illumina Miseq by purifying DNA using the Zymoprep yeast plasmid prep II (Zymo Research), and PCR amplification for 12 cycles. .. The endogenous promoter of HIS3 was replaced from -1 to -122 bp upstream from the start codon with a single tetO site derived from the previously published construct pCM188 .

    Article Title: Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus
    Article Snippet: Yeast propagation was performed in the presence of 2% raffinose + 0.1% glucose at 30°C for at least 12 h prior to induction. .. Plasmids were isolated from yeast populations using the Zymoprep-II kit (Zymo Research) and transformed into Escherichia coli DH5α by heat shock for amplification and/or sequencing. .. Sequencing was performed on 40–60 clones for a given selection output.

    Binding Assay:

    Article Title: Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis
    Article Snippet: Paragraph title: Library screening for MBD2 variants with improved binding affinity to methylated CpGs ... After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies).

    Article Title: Adnectin–drug conjugates for Glypican-3-specific delivery of a cytotoxic payload to tumors
    Article Snippet: Paragraph title: Discovery of Glypican-3 -binding Adnectins ... Plasmids containing the genes of enriched Adnectins were recovered from the post-round-4 yeast population (in the 0.15% gate) using Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research D2004).

    DNA Extraction:

    Article Title: Efficient proximity labeling in living cells and organisms with TurboID
    Article Snippet: For negative selections , gates were drawn to collect yeast with AF647 signal and no PE signal above background ( ). .. After sorting, yeast were collected in SDCAA medium containing 1% penicillin-streptomycin and incubated at 30°C for 24 h. 1 mL of the growing culture was removed for DNA extraction using the Zymoprep yeast Plasmid Miniprep II (Zymo Research) kit according to manufacturer protocols (using 6 μL zymolyase, vigorously vortex after lysis), and at least ten-fold excess of the number of cells retained during sorting were propagated in SDCAA + 1% pen-strep to ensure oversampling (yeast cells were passaged in this manner at least two times prior to the next round of selection). .. To analyze yeast populations and clones by FACS ( ; ), yeast samples were prepared on a small scale (1 mL cultures) as described above, and analyzed on a BD Accuri flow cytometer (BD Biosciences).

    Molecular Cloning:

    Article Title: Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen
    Article Snippet: DNA sequences were verified by Genewiz, Inc. E scherichia coli strains DH5α, 10-β electrocompetent (NEB) were used as hosts for molecular cloning. .. DNA purification from yeast was performed using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    In Vivo:

    Article Title: Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast
    Article Snippet: In vivo yeast recombination cloning was carried out using a Frozen-EZ Yeast Transformation II Kit™ (Zymo Research) where competent S. cerevisiae BJ5464 [ ] was transformed with the DNA fragments (PCR products) of the respective genes and linearized plasmid backbone derived from YEplac-ADH2p [ , ]. .. Plasmid DNA was isolated from positive transformants using a Zymoprep™ Yeast Plasmid Miniprep II Kit (Zymo Research) and used to transform NEB 5-alpha Electrocompetent E. coli (New England Biolabs) by electroporation.

    Fluorescence:

    Article Title: Adnectin–drug conjugates for Glypican-3-specific delivery of a cytotoxic payload to tumors
    Article Snippet: Fluorescence-activated cell sorter BD FACSAria II was used to capture the yeast cells with the optimal combination of display and binding signal. .. Plasmids containing the genes of enriched Adnectins were recovered from the post-round-4 yeast population (in the 0.15% gate) using Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research D2004).

    Methylation:

    Article Title: Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis
    Article Snippet: Paragraph title: Library screening for MBD2 variants with improved binding affinity to methylated CpGs ... After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies).

    Mutagenesis:

    Article Title: Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis
    Article Snippet: After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies). .. Individual clones were isolated and the MBD2 gene was sequenced using the forward primer 5′-CCC CTC AAC TAG CAA AGG CAG-3′.

    Article Title: Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen
    Article Snippet: Site-directed mutagenesis was performed with Turbo pfu polymerase (Agilent). .. DNA purification from yeast was performed using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    Article Title: Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding
    Article Snippet: Plasmid DNA from the enriched library was recovered using a Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) following manufacturer’s protocol, transformed into bacteria, and individual clones were sequenced by standard Sanger DNA sequencing methods. .. Plasmid DNA from the enriched library was recovered using a Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) following manufacturer’s protocol, transformed into bacteria, and individual clones were sequenced by standard Sanger DNA sequencing methods.

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: By using different amounts of template DNA, 2 libraries differing in their mutation rates were constructed. .. After growing the S. cerevisiae -libraries in SD-CAA-medium [20 g/l glucose, 0.1 M KH2 PO4 /K2 HPO4 , pH 6, 10 g/l (NH4 )2 SO4 , 0.1 g/l l -leucine (all from Sigma, St. Louis, MO), 3.4 g/l yeast nitrogen base, 10 g/l bacto casamino acids (both from Difco, BD, Franklin Lakes, NJ)] at 28 °C for 48 h, pYD1 plasmid DNA was isolated by using the Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research, Orange, CA) and transformed into Escherichia coli Top 10 for sequencing.

    Article Title: Identification of Ci
    Article Snippet: The 5′- or 3′-UTRs of mutant replicons were amplified from the colonies, and their sequences were verified (MC Lab, South San Francisco, CA). .. Plasmid DNAs harboring the mutations were recovered using the Zymoprep II yeast plasmid minipreparation kit (Zymo Research), and 2 μl were used to transform 20 μl of MAX Efficiency Stbl2-competent cells (Invitrogen).

    Article Title: Improving Saccharomyces cerevisiae ethanol production and tolerance via RNA polymerase II subunit Rpb7
    Article Snippet: Paragraph title: Mutant identification ... Individual colonies were randomly picked for miniprep [Zymoprep II kit (Zymo Research, Orange, CA, USA)] and sent for DNA sequencing.

    Isolation:

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: The subsequent 2 rounds of selection were performed in a similar way, except that the concentration of ricin A chain used was decreased to 200 nM and 40 nM, respectively. .. After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research). .. Plasmids were amplified in E. coli DH10β and sequenced.

    Article Title: Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast
    Article Snippet: Yeast transformants grown on synthetic dropout agar plate lacking uracil were screened by PCR. .. Plasmid DNA was isolated from positive transformants using a Zymoprep™ Yeast Plasmid Miniprep II Kit (Zymo Research) and used to transform NEB 5-alpha Electrocompetent E. coli (New England Biolabs) by electroporation. .. Plasmid DNA was isolated from the positive clones grown on LB-ampicillin using the alkaline lysis method and further verified by DNA sequencing.

    Article Title: L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast
    Article Snippet: For experiments carried out with yeast strain EST-Cre2, all colonies were counted from one plate of each replicate. .. Plasmids were isolated from yeast colonies using the Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) and subsequently retransformed into E. coli strain DH5α. .. After plasmid purification from E. coli , plasmids were digested with Pst I and Sac I and obtained fragments were separated via agarose gel electrophoresis.

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: The library inserts comprised homologous regions to the BamHI/NotI-digested pYD1 backbone on both sides in order to facilitate gap repair driven homologous recombination in S. cerevisiae . .. After growing the S. cerevisiae -libraries in SD-CAA-medium [20 g/l glucose, 0.1 M KH2 PO4 /K2 HPO4 , pH 6, 10 g/l (NH4 )2 SO4 , 0.1 g/l l -leucine (all from Sigma, St. Louis, MO), 3.4 g/l yeast nitrogen base, 10 g/l bacto casamino acids (both from Difco, BD, Franklin Lakes, NJ)] at 28 °C for 48 h, pYD1 plasmid DNA was isolated by using the Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research, Orange, CA) and transformed into Escherichia coli Top 10 for sequencing. .. Furthermore, cell surface expression was induced and analyzed using flow cytometry as described below.

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: If the number of sorted cells was below 5 × 105 , non-transformed EBY100 cells (not containing any pYD1 plasmid) were added before centrifugation in order to facilitate the formation of a cell pellet. .. After washing the cells with PBS/BSA, the pYD1-Fc-library DNA was isolated from S. cerevisiae by using the Zymoprep Yeast Plasmid Miniprep Kit II with some modifications of the manufacturer's protocol. .. In detail, the cell suspension was incubated at 37 °C for 60 min with twice the recommended amount of zymolyase.

    Article Title: Cloning of the Repertoire of Individual Plasmodium falciparum var Genes Using Transformation Associated Recombination (TAR)
    Article Snippet: All yeast TAR clones were propagated on selective medium and yeast genomic DNA was isolated by phenol/chloroform purification (as described in ) with subsequent precipitation. .. Alternatively, yeast plasmid DNA was directly purified using the Zymoprep II™ Yeast Plasmid Miniprep Kit (Zymo Research) or the QIAprep Spin Miniprep Kit (Qiagen).

    Article Title: AhR/Arnt:XRE interaction: Turning false negatives into true positives in the modified yeast one-hybrid assay
    Article Snippet: Transformants were selected by leucine prototrophy. .. Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA). .. Polymerase chain reactions (PCRs) were performed with Phusion high-fidelity DNA polymerase (New England Biolabs).

    Article Title: Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus
    Article Snippet: Yeast propagation was performed in the presence of 2% raffinose + 0.1% glucose at 30°C for at least 12 h prior to induction. .. Plasmids were isolated from yeast populations using the Zymoprep-II kit (Zymo Research) and transformed into Escherichia coli DH5α by heat shock for amplification and/or sequencing. .. Sequencing was performed on 40–60 clones for a given selection output.

    Size-exclusion Chromatography:

    Article Title: Cloning of the Repertoire of Individual Plasmodium falciparum var Genes Using Transformation Associated Recombination (TAR)
    Article Snippet: Alternatively, yeast plasmid DNA was directly purified using the Zymoprep II™ Yeast Plasmid Miniprep Kit (Zymo Research) or the QIAprep Spin Miniprep Kit (Qiagen). .. Alternatively, yeast plasmid DNA was directly purified using the Zymoprep II™ Yeast Plasmid Miniprep Kit (Zymo Research) or the QIAprep Spin Miniprep Kit (Qiagen).

    Labeling:

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: For the 2nd round of selection, 107 cells in 200 μl PBS+0.1% BSA (PBSF) were labeled with 1 μM biotinylated ricin A chain and 4 μg/ml chicken anti-c-Myc IgY at RT for 1hr. .. After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    Purification:

    Article Title: In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity
    Article Snippet: Plasmid was extracted from at least 107 yeast cells per sample using Zymoprep Yeast Plasmid Miniprep II (Zymo Research, Irvine, CA) according to the manufacturer's instructions. .. Plasmid was extracted from at least 107 yeast cells per sample using Zymoprep Yeast Plasmid Miniprep II (Zymo Research, Irvine, CA) according to the manufacturer's instructions.

    Article Title: Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen
    Article Snippet: DNA plasmid purification from bacteria was performed using QIAPrep Spin Miniprep (Qiagen), Zyppy Plasmid Midiprep (Zymo Research) or E.Z.N.A. .. DNA purification from yeast was performed using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    Article Title: Cloning of the Repertoire of Individual Plasmodium falciparum var Genes Using Transformation Associated Recombination (TAR)
    Article Snippet: All yeast TAR clones were propagated on selective medium and yeast genomic DNA was isolated by phenol/chloroform purification (as described in ) with subsequent precipitation. .. Alternatively, yeast plasmid DNA was directly purified using the Zymoprep II™ Yeast Plasmid Miniprep Kit (Zymo Research) or the QIAprep Spin Miniprep Kit (Qiagen). .. Genomic DNA of yeast TAR clones was digested with NotI and separated on 1% agarose gels in 0.5 x TBE using a CHEF mapper system (BIORAD) with the following conditions: forward: 9 V/cm, 10 s initial switch, 40 s final switch, reverse: 6 V/cm, 10 s initial switch, 40 s final switch, for 24 hrs at 14°C.

    Article Title: AhR/Arnt:XRE interaction: Turning false negatives into true positives in the modified yeast one-hybrid assay
    Article Snippet: Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA). .. Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA).

    Article Title: A tetO toolkit to alter expression of genes in Saccharomyces cerevisiae
    Article Snippet: Deep sequencing of plasmid DNA was performed on an Illumina Miseq by purifying DNA using the Zymoprep yeast plasmid prep II (Zymo Research), and PCR amplification for 12 cycles. .. Deep sequencing of plasmid DNA was performed on an Illumina Miseq by purifying DNA using the Zymoprep yeast plasmid prep II (Zymo Research), and PCR amplification for 12 cycles.

    Article Title: Identification of Ci
    Article Snippet: These were purified by phenol/chloroform/isoamyl alcohol (25:24:1), ethanol-precipitated, and resuspended in 5 μl of water. .. Plasmid DNAs harboring the mutations were recovered using the Zymoprep II yeast plasmid minipreparation kit (Zymo Research), and 2 μl were used to transform 20 μl of MAX Efficiency Stbl2-competent cells (Invitrogen).

    Polymerase Chain Reaction:

    Article Title: Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide
    Article Snippet: The PCR products were mixed with pCTCON2 plasmid that was digested with NheI and SalI, and transformed into the EBY100 strain for homologous recombination and selection on SD-CAA agar plates. .. Overnight yeast cell cultures were miniprepped (D2004, Zymoprep II yeast miniprep kit, Zymo Research) and subsequently transformed into electroporation competent XL1-blue bacterial cells (200228, Agilent Technologies).

    Article Title: In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity
    Article Snippet: Plasmid was extracted from at least 107 yeast cells per sample using Zymoprep Yeast Plasmid Miniprep II (Zymo Research, Irvine, CA) according to the manufacturer's instructions. .. The mutated region on the C05 heavy chain was amplified by PCR using KOD DNA polymerase (EMD Millipore) with 1.5 mM MgSO4 , 0.2 mM of each dNTP (dATP, dCTP, dGTP and dTTP), and 0.5 μM each of the primers 5′-CACTCTTTCCCTACACGACGCTCTTCCGATCTACCGGTGTGTACTACTGCGCTAAGC-3′ and 5′-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCCCCACACATCGAAGGCGTCACCC-3′.

    Article Title: Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast
    Article Snippet: Yeast transformants grown on synthetic dropout agar plate lacking uracil were screened by PCR. .. Plasmid DNA was isolated from positive transformants using a Zymoprep™ Yeast Plasmid Miniprep II Kit (Zymo Research) and used to transform NEB 5-alpha Electrocompetent E. coli (New England Biolabs) by electroporation.

    Article Title: Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding
    Article Snippet: Plasmid DNA from the enriched library was recovered using a Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) following manufacturer’s protocol, transformed into bacteria, and individual clones were sequenced by standard Sanger DNA sequencing methods. .. Plasmid DNA was subsequently mutated by error-prone PCR of either the entire Fn3 gene or the paratope loops using nucleotide analogues, 8-oxo-2’-deoxyguanosine-5’-triphosphate (8-oxo-dGTP) (TriLink Biotechnologies) and 2’deoxy-p-nucleoside-5’-triphosphate (dPTP) (TriLink Biotechnologies) [ ].

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: This pYD1-Fc plasmid was used as the template for error prone PCR (GeneMorph II Random Mutagenesis Kit, Stratagene, La Jolla, CA). .. After growing the S. cerevisiae -libraries in SD-CAA-medium [20 g/l glucose, 0.1 M KH2 PO4 /K2 HPO4 , pH 6, 10 g/l (NH4 )2 SO4 , 0.1 g/l l -leucine (all from Sigma, St. Louis, MO), 3.4 g/l yeast nitrogen base, 10 g/l bacto casamino acids (both from Difco, BD, Franklin Lakes, NJ)] at 28 °C for 48 h, pYD1 plasmid DNA was isolated by using the Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research, Orange, CA) and transformed into Escherichia coli Top 10 for sequencing.

    Article Title: Cloning of the Repertoire of Individual Plasmodium falciparum var Genes Using Transformation Associated Recombination (TAR)
    Article Snippet: Alternatively, yeast plasmid DNA was directly purified using the Zymoprep II™ Yeast Plasmid Miniprep Kit (Zymo Research) or the QIAprep Spin Miniprep Kit (Qiagen). .. Alternatively, yeast plasmid DNA was directly purified using the Zymoprep II™ Yeast Plasmid Miniprep Kit (Zymo Research) or the QIAprep Spin Miniprep Kit (Qiagen).

    Article Title: AhR/Arnt:XRE interaction: Turning false negatives into true positives in the modified yeast one-hybrid assay
    Article Snippet: Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA). .. Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA).

    Article Title: A tetO toolkit to alter expression of genes in Saccharomyces cerevisiae
    Article Snippet: Sanger sequence and analysis was performed as previously described . .. Deep sequencing of plasmid DNA was performed on an Illumina Miseq by purifying DNA using the Zymoprep yeast plasmid prep II (Zymo Research), and PCR amplification for 12 cycles. .. The endogenous promoter of HIS3 was replaced from -1 to -122 bp upstream from the start codon with a single tetO site derived from the previously published construct pCM188 .

    Article Title: Identification of Ci
    Article Snippet: The linearized WT or the mutant replicon plasmid was mixed with the vacuum-dried mutant PCR fragments, and the mixture was introduced into Saccharomyces cerevisiae YPH857 (50 μl) made chemically competent using the S.c. EasyComp Transformation Kit (Invitrogen) ( ). .. Plasmid DNAs harboring the mutations were recovered using the Zymoprep II yeast plasmid minipreparation kit (Zymo Research), and 2 μl were used to transform 20 μl of MAX Efficiency Stbl2-competent cells (Invitrogen).

    Article Title: Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus
    Article Snippet: For random mutagenesis library construction, error-prone PCR was performed over selected region of the I-Anil variant using the GeneMorph-II Random Mutagenesis kit (Stratagene) according to the manufacturer's protocol. .. Plasmids were isolated from yeast populations using the Zymoprep-II kit (Zymo Research) and transformed into Escherichia coli DH5α by heat shock for amplification and/or sequencing.

    Selection:

    Article Title: Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide
    Article Snippet: The PCR products were mixed with pCTCON2 plasmid that was digested with NheI and SalI, and transformed into the EBY100 strain for homologous recombination and selection on SD-CAA agar plates. .. Overnight yeast cell cultures were miniprepped (D2004, Zymoprep II yeast miniprep kit, Zymo Research) and subsequently transformed into electroporation competent XL1-blue bacterial cells (200228, Agilent Technologies).

    Article Title: Efficient proximity labeling in living cells and organisms with TurboID
    Article Snippet: For negative selections , gates were drawn to collect yeast with AF647 signal and no PE signal above background ( ). .. After sorting, yeast were collected in SDCAA medium containing 1% penicillin-streptomycin and incubated at 30°C for 24 h. 1 mL of the growing culture was removed for DNA extraction using the Zymoprep yeast Plasmid Miniprep II (Zymo Research) kit according to manufacturer protocols (using 6 μL zymolyase, vigorously vortex after lysis), and at least ten-fold excess of the number of cells retained during sorting were propagated in SDCAA + 1% pen-strep to ensure oversampling (yeast cells were passaged in this manner at least two times prior to the next round of selection). .. To analyze yeast populations and clones by FACS ( ; ), yeast samples were prepared on a small scale (1 mL cultures) as described above, and analyzed on a BD Accuri flow cytometer (BD Biosciences).

    Article Title: Adnectin–drug conjugates for Glypican-3-specific delivery of a cytotoxic payload to tumors
    Article Snippet: Plasmids containing the genes of enriched Adnectins were recovered from the post-round-4 yeast population (in the 0.15% gate) using Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research D2004). .. Plasmids containing the genes of enriched Adnectins were recovered from the post-round-4 yeast population (in the 0.15% gate) using Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research D2004).

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: The subsequent 2 rounds of selection were performed in a similar way, except that the concentration of ricin A chain used was decreased to 200 nM and 40 nM, respectively. .. After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research). .. Plasmids were amplified in E. coli DH10β and sequenced.

    Recombinant:

    Article Title: AhR/Arnt:XRE interaction: Turning false negatives into true positives in the modified yeast one-hybrid assay
    Article Snippet: Recombinant plasmids were transformed into E. coli by the standard transformation and storage solution (TSS) procedure [ ]. .. Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA).

    Lysis:

    Article Title: Efficient proximity labeling in living cells and organisms with TurboID
    Article Snippet: For negative selections , gates were drawn to collect yeast with AF647 signal and no PE signal above background ( ). .. After sorting, yeast were collected in SDCAA medium containing 1% penicillin-streptomycin and incubated at 30°C for 24 h. 1 mL of the growing culture was removed for DNA extraction using the Zymoprep yeast Plasmid Miniprep II (Zymo Research) kit according to manufacturer protocols (using 6 μL zymolyase, vigorously vortex after lysis), and at least ten-fold excess of the number of cells retained during sorting were propagated in SDCAA + 1% pen-strep to ensure oversampling (yeast cells were passaged in this manner at least two times prior to the next round of selection). .. To analyze yeast populations and clones by FACS ( ; ), yeast samples were prepared on a small scale (1 mL cultures) as described above, and analyzed on a BD Accuri flow cytometer (BD Biosciences).

    Plasmid Preparation:

    Article Title: Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide
    Article Snippet: The PCR products were mixed with pCTCON2 plasmid that was digested with NheI and SalI, and transformed into the EBY100 strain for homologous recombination and selection on SD-CAA agar plates. .. Overnight yeast cell cultures were miniprepped (D2004, Zymoprep II yeast miniprep kit, Zymo Research) and subsequently transformed into electroporation competent XL1-blue bacterial cells (200228, Agilent Technologies).

    Article Title: In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity
    Article Snippet: Yeast colonies were collected after 2 days of incubation at 30 °C, resuspended in YPD with 15% glycerol, and stored at −80 °C until use. .. Plasmid was extracted from at least 107 yeast cells per sample using Zymoprep Yeast Plasmid Miniprep II (Zymo Research, Irvine, CA) according to the manufacturer's instructions. .. The mutated region on the C05 heavy chain was amplified by PCR using KOD DNA polymerase (EMD Millipore) with 1.5 mM MgSO4 , 0.2 mM of each dNTP (dATP, dCTP, dGTP and dTTP), and 0.5 μM each of the primers 5′-CACTCTTTCCCTACACGACGCTCTTCCGATCTACCGGTGTGTACTACTGCGCTAAGC-3′ and 5′-GACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCCCCACACATCGAAGGCGTCACCC-3′.

    Article Title: Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis
    Article Snippet: A 10-fold oversampling of the expanded cells was re-suspended in SGCAA media for surface display fusion expression and sorting in the next round of screening. .. After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies). .. Individual clones were isolated and the MBD2 gene was sequenced using the forward primer 5′-CCC CTC AAC TAG CAA AGG CAG-3′.

    Article Title: Efficient proximity labeling in living cells and organisms with TurboID
    Article Snippet: For negative selections , gates were drawn to collect yeast with AF647 signal and no PE signal above background ( ). .. After sorting, yeast were collected in SDCAA medium containing 1% penicillin-streptomycin and incubated at 30°C for 24 h. 1 mL of the growing culture was removed for DNA extraction using the Zymoprep yeast Plasmid Miniprep II (Zymo Research) kit according to manufacturer protocols (using 6 μL zymolyase, vigorously vortex after lysis), and at least ten-fold excess of the number of cells retained during sorting were propagated in SDCAA + 1% pen-strep to ensure oversampling (yeast cells were passaged in this manner at least two times prior to the next round of selection). .. To analyze yeast populations and clones by FACS ( ; ), yeast samples were prepared on a small scale (1 mL cultures) as described above, and analyzed on a BD Accuri flow cytometer (BD Biosciences).

    Article Title: Adnectin–drug conjugates for Glypican-3-specific delivery of a cytotoxic payload to tumors
    Article Snippet: The fraction of yeast population captured in rounds 1–4 was 2.6, 0.5, 0.5 and 0.15%. .. Plasmids containing the genes of enriched Adnectins were recovered from the post-round-4 yeast population (in the 0.15% gate) using Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research D2004). .. The Adnectin genes were subcloned into plasmid pET9d, sequenced, then expressed and screened in 96-plate format ( ).

    Article Title: Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen
    Article Snippet: Plasmid Mega kits (Omega Bio-tek). .. DNA purification from yeast was performed using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research). .. Antibodies: The following reagents were obtained through the NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: CH58 and CH59 from Drs Barton F. Haynes and Hua-Xin Liao ( ; ); anti-HIV-1 gp120 Monoclonal (697-30D) from Dr. Susan Zolla-Pazner ( ; ; ); anti-HIV-1 gp120 Monoclonal (PGT145) ( ); catalog #3957, HIV-IG from NABI and NHLBI.

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: The subsequent 2 rounds of selection were performed in a similar way, except that the concentration of ricin A chain used was decreased to 200 nM and 40 nM, respectively. .. After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research). .. Plasmids were amplified in E. coli DH10β and sequenced.

    Article Title: Heterologous expression of cytotoxic sesquiterpenoids from the medicinal mushroom Lignosus rhinocerotis in yeast
    Article Snippet: Yeast transformants grown on synthetic dropout agar plate lacking uracil were screened by PCR. .. Plasmid DNA was isolated from positive transformants using a Zymoprep™ Yeast Plasmid Miniprep II Kit (Zymo Research) and used to transform NEB 5-alpha Electrocompetent E. coli (New England Biolabs) by electroporation. .. Plasmid DNA was isolated from the positive clones grown on LB-ampicillin using the alkaline lysis method and further verified by DNA sequencing.

    Article Title: Fn3 proteins engineered to recognize tumor biomarker mesothelin internalize upon binding
    Article Snippet: Four iterative rounds of enrichment were performed. .. Plasmid DNA from the enriched library was recovered using a Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) following manufacturer’s protocol, transformed into bacteria, and individual clones were sequenced by standard Sanger DNA sequencing methods. .. Plasmid DNA was subsequently mutated by error-prone PCR of either the entire Fn3 gene or the paratope loops using nucleotide analogues, 8-oxo-2’-deoxyguanosine-5’-triphosphate (8-oxo-dGTP) (TriLink Biotechnologies) and 2’deoxy-p-nucleoside-5’-triphosphate (dPTP) (TriLink Biotechnologies) [ ].

    Article Title: L-SCRaMbLE as a tool for light-controlled Cre-mediated recombination in yeast
    Article Snippet: For experiments carried out with yeast strain EST-Cre2, all colonies were counted from one plate of each replicate. .. Plasmids were isolated from yeast colonies using the Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research) and subsequently retransformed into E. coli strain DH5α. .. After plasmid purification from E. coli , plasmids were digested with Pst I and Sac I and obtained fragments were separated via agarose gel electrophoresis.

    Article Title: Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach
    Article Snippet: E. coli minipreps were performed by using the Zyppy plasmid miniprep kit (Zymo Research Corporation). .. Y. lipolytica minipreps were performed by using a Zymoprep yeast plasmid miniprep II kit (Zymo Research Corporation). .. The transformation of E. coli strains was performed by using standard electroporator protocols ( ).

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: The library inserts comprised homologous regions to the BamHI/NotI-digested pYD1 backbone on both sides in order to facilitate gap repair driven homologous recombination in S. cerevisiae . .. After growing the S. cerevisiae -libraries in SD-CAA-medium [20 g/l glucose, 0.1 M KH2 PO4 /K2 HPO4 , pH 6, 10 g/l (NH4 )2 SO4 , 0.1 g/l l -leucine (all from Sigma, St. Louis, MO), 3.4 g/l yeast nitrogen base, 10 g/l bacto casamino acids (both from Difco, BD, Franklin Lakes, NJ)] at 28 °C for 48 h, pYD1 plasmid DNA was isolated by using the Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research, Orange, CA) and transformed into Escherichia coli Top 10 for sequencing. .. Furthermore, cell surface expression was induced and analyzed using flow cytometry as described below.

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: If the number of sorted cells was below 5 × 105 , non-transformed EBY100 cells (not containing any pYD1 plasmid) were added before centrifugation in order to facilitate the formation of a cell pellet. .. After washing the cells with PBS/BSA, the pYD1-Fc-library DNA was isolated from S. cerevisiae by using the Zymoprep Yeast Plasmid Miniprep Kit II with some modifications of the manufacturer's protocol. .. In detail, the cell suspension was incubated at 37 °C for 60 min with twice the recommended amount of zymolyase.

    Article Title: Cloning of the Repertoire of Individual Plasmodium falciparum var Genes Using Transformation Associated Recombination (TAR)
    Article Snippet: All yeast TAR clones were propagated on selective medium and yeast genomic DNA was isolated by phenol/chloroform purification (as described in ) with subsequent precipitation. .. Alternatively, yeast plasmid DNA was directly purified using the Zymoprep II™ Yeast Plasmid Miniprep Kit (Zymo Research) or the QIAprep Spin Miniprep Kit (Qiagen). .. Genomic DNA of yeast TAR clones was digested with NotI and separated on 1% agarose gels in 0.5 x TBE using a CHEF mapper system (BIORAD) with the following conditions: forward: 9 V/cm, 10 s initial switch, 40 s final switch, reverse: 6 V/cm, 10 s initial switch, 40 s final switch, for 24 hrs at 14°C.

    Article Title: AhR/Arnt:XRE interaction: Turning false negatives into true positives in the modified yeast one-hybrid assay
    Article Snippet: Transformants were selected by leucine prototrophy. .. Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA). .. Polymerase chain reactions (PCRs) were performed with Phusion high-fidelity DNA polymerase (New England Biolabs).

    Article Title: A tetO toolkit to alter expression of genes in Saccharomyces cerevisiae
    Article Snippet: Sanger sequence and analysis was performed as previously described . .. Deep sequencing of plasmid DNA was performed on an Illumina Miseq by purifying DNA using the Zymoprep yeast plasmid prep II (Zymo Research), and PCR amplification for 12 cycles. .. The endogenous promoter of HIS3 was replaced from -1 to -122 bp upstream from the start codon with a single tetO site derived from the previously published construct pCM188 .

    Article Title: Identification of Ci
    Article Snippet: The 5′- or 3′-UTRs of mutant replicons were amplified from the colonies, and their sequences were verified (MC Lab, South San Francisco, CA). .. Plasmid DNAs harboring the mutations were recovered using the Zymoprep II yeast plasmid minipreparation kit (Zymo Research), and 2 μl were used to transform 20 μl of MAX Efficiency Stbl2-competent cells (Invitrogen). .. Replicon plasmids were propagated in Escherichia coli from single colonies, and their sequences within 5′- and 3′-UTRs were again verified.

    Article Title: Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus
    Article Snippet: Paragraph title: Yeast growth, transformation, library construction and plasmid recovery ... Plasmids were isolated from yeast populations using the Zymoprep-II kit (Zymo Research) and transformed into Escherichia coli DH5α by heat shock for amplification and/or sequencing.

    Software:

    Article Title: Efficient proximity labeling in living cells and organisms with TurboID
    Article Snippet: After sorting, yeast were collected in SDCAA medium containing 1% penicillin-streptomycin and incubated at 30°C for 24 h. 1 mL of the growing culture was removed for DNA extraction using the Zymoprep yeast Plasmid Miniprep II (Zymo Research) kit according to manufacturer protocols (using 6 μL zymolyase, vigorously vortex after lysis), and at least ten-fold excess of the number of cells retained during sorting were propagated in SDCAA + 1% pen-strep to ensure oversampling (yeast cells were passaged in this manner at least two times prior to the next round of selection). .. To analyze yeast populations and clones by FACS ( ; ), yeast samples were prepared on a small scale (1 mL cultures) as described above, and analyzed on a BD Accuri flow cytometer (BD Biosciences).

    Multiplex Assay:

    Article Title: In vitro evolution of an influenza broadly neutralizing antibody is modulated by hemagglutinin receptor specificity
    Article Snippet: Plasmid was extracted from at least 107 yeast cells per sample using Zymoprep Yeast Plasmid Miniprep II (Zymo Research, Irvine, CA) according to the manufacturer's instructions. .. The purified product was used as a template for a second PCR performed under the same conditions except that primers 5′-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCT-3′ and 5′-CAAGCAGAAGACGGCATACGAGAT NNNNNN GTGACTGGAGTTCAGACGTGTGCT-3′ were used instead.

    Positron Emission Tomography:

    Article Title: Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide
    Article Snippet: Aga2-VH fusions were subcloned from existing pET-17b constructs using PCR amplification to introduce overhangs complementary to the pCTCON2 yeast display plasmid. .. Overnight yeast cell cultures were miniprepped (D2004, Zymoprep II yeast miniprep kit, Zymo Research) and subsequently transformed into electroporation competent XL1-blue bacterial cells (200228, Agilent Technologies).

    FACS:

    Article Title: Characterization and directed evolution of a methyl-binding domain protein for high-sensitivity DNA methylation analysis
    Article Snippet: A 10-fold oversampling of the expanded cells was re-suspended in SGCAA media for surface display fusion expression and sorting in the next round of screening. .. After the third round of FACS, the plasmids encoding the MBD2-derived variants were collected using the Zymoprep™ Yeast Plasmid Miniprep II (Zymo Research) and transformed into Mach 1 E.coli cells (Life Technologies). .. Individual clones were isolated and the MBD2 gene was sequenced using the forward primer 5′-CCC CTC AAC TAG CAA AGG CAG-3′.

    Article Title: Efficient proximity labeling in living cells and organisms with TurboID
    Article Snippet: After sorting, yeast were collected in SDCAA medium containing 1% penicillin-streptomycin and incubated at 30°C for 24 h. 1 mL of the growing culture was removed for DNA extraction using the Zymoprep yeast Plasmid Miniprep II (Zymo Research) kit according to manufacturer protocols (using 6 μL zymolyase, vigorously vortex after lysis), and at least ten-fold excess of the number of cells retained during sorting were propagated in SDCAA + 1% pen-strep to ensure oversampling (yeast cells were passaged in this manner at least two times prior to the next round of selection). .. To analyze yeast populations and clones by FACS ( ; ), yeast samples were prepared on a small scale (1 mL cultures) as described above, and analyzed on a BD Accuri flow cytometer (BD Biosciences).

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: After washing with PBSF, cells were incubated with 5 μg/ml SA-633 and 5 μg/ml GaC-488 at 4°C for 30 min. After washing, cells were resuspended in PBSF buffer and sorted using FACS Aria (BD Bioscience). .. After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    Concentration Assay:

    Article Title: Discovery of high affinity anti-ricin antibodies by B cell receptor sequencing and by yeast display of combinatorial VH:VL libraries from immunized animals
    Article Snippet: The subsequent 2 rounds of selection were performed in a similar way, except that the concentration of ricin A chain used was decreased to 200 nM and 40 nM, respectively. .. After 4 rounds of selection, 20 random colonies from each library were picked, and plasmids were isolated using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    Article Title: Improving Saccharomyces cerevisiae ethanol production and tolerance via RNA polymerase II subunit Rpb7
    Article Snippet: The mutant library was cultured in 200 mL YPAD medium supplemented with elevated ethanol concentration [from 8 to 12% (v/v)]. .. Individual colonies were randomly picked for miniprep [Zymoprep II kit (Zymo Research, Orange, CA, USA)] and sent for DNA sequencing.

    DNA Purification:

    Article Title: Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen
    Article Snippet: Plasmid Mega kits (Omega Bio-tek). .. DNA purification from yeast was performed using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research). .. Antibodies: The following reagents were obtained through the NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH: CH58 and CH59 from Drs Barton F. Haynes and Hua-Xin Liao ( ; ); anti-HIV-1 gp120 Monoclonal (697-30D) from Dr. Susan Zolla-Pazner ( ; ; ); anti-HIV-1 gp120 Monoclonal (PGT145) ( ); catalog #3957, HIV-IG from NABI and NHLBI.

    Article Title: Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach
    Article Snippet: Y. lipolytica minipreps were performed by using a Zymoprep yeast plasmid miniprep II kit (Zymo Research Corporation). .. The transformation of Y. lipolytica was performed by using Zymogen Frozen EZ yeast transformation kit II (Zymo Research Corporation).

    Article Title: AhR/Arnt:XRE interaction: Turning false negatives into true positives in the modified yeast one-hybrid assay
    Article Snippet: Plasmids were isolated using the Wizard Plus SV Minipreps DNA Purification System (Promega, Madison, WI, USA). .. Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA).

    Gel Extraction:

    Article Title: Towards conformational fidelity of a quaternary HIV-1 epitope: computational design and directed evolution of a minimal V1V2 antigen
    Article Snippet: Phusion DNA Polymerase, Taq polymerase, DNA restriction and ligation enzymes were purchased from New England Biolabs (NEB), and DNA purification and gel-extraction were performed using Geneaid kits. .. DNA purification from yeast was performed using Zymoprep Yeast Plasmid Miniprep II kit (Zymo Research).

    Article Title: Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach
    Article Snippet: Gel extractions were performed by using the GeneClean gel extraction kit, purchased from MP Biomedicals. .. Y. lipolytica minipreps were performed by using a Zymoprep yeast plasmid miniprep II kit (Zymo Research Corporation).

    Article Title: AhR/Arnt:XRE interaction: Turning false negatives into true positives in the modified yeast one-hybrid assay
    Article Snippet: Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA). .. Isolation of yeast plasmids was performed using the Zymoprep II Yeast Plasmid Miniprep Kit (Zymo Research, Orange, CA, USA).

    Variant Assay:

    Article Title: Progressive engineering of a homing endonuclease genome editing reagent for the murine X-linked immunodeficiency locus
    Article Snippet: For random mutagenesis library construction, error-prone PCR was performed over selected region of the I-Anil variant using the GeneMorph-II Random Mutagenesis kit (Stratagene) according to the manufacturer's protocol. .. Plasmids were isolated from yeast populations using the Zymoprep-II kit (Zymo Research) and transformed into Escherichia coli DH5α by heat shock for amplification and/or sequencing.

    Homologous Recombination:

    Article Title: Design and Optimization of Anti-amyloid Domain Antibodies Specific for β-Amyloid and Islet Amyloid Polypeptide
    Article Snippet: The PCR products were mixed with pCTCON2 plasmid that was digested with NheI and SalI, and transformed into the EBY100 strain for homologous recombination and selection on SD-CAA agar plates. .. Overnight yeast cell cultures were miniprepped (D2004, Zymoprep II yeast miniprep kit, Zymo Research) and subsequently transformed into electroporation competent XL1-blue bacterial cells (200228, Agilent Technologies).

    Article Title: Directed evolution of stabilized IgG1-Fc scaffolds by application of strong heat shock to libraries displayed on yeast
    Article Snippet: The library inserts comprised homologous regions to the BamHI/NotI-digested pYD1 backbone on both sides in order to facilitate gap repair driven homologous recombination in S. cerevisiae . .. After growing the S. cerevisiae -libraries in SD-CAA-medium [20 g/l glucose, 0.1 M KH2 PO4 /K2 HPO4 , pH 6, 10 g/l (NH4 )2 SO4 , 0.1 g/l l -leucine (all from Sigma, St. Louis, MO), 3.4 g/l yeast nitrogen base, 10 g/l bacto casamino acids (both from Difco, BD, Franklin Lakes, NJ)] at 28 °C for 48 h, pYD1 plasmid DNA was isolated by using the Zymoprep Yeast Plasmid Miniprep Kit II (Zymo Research, Orange, CA) and transformed into Escherichia coli Top 10 for sequencing.

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    Zymo Research plasmid miniprep classic kit
    Plasmid Miniprep Classic Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 96/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/plasmid miniprep classic kit/product/Zymo Research
    Average 96 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    plasmid miniprep classic kit - by Bioz Stars, 2019-12
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    99
    Zymo Research zr duet rna dna miniprep kit
    GC content and dinucleotide composition are associated with regulatory activity in U87 cells and hNPCs. ( A, D ) Distributions of expression values for all cis- regulatory elements in U87 cells (A) and hNPCs (D). Expression values are averaged across the three biological replicates and plotted as log 2 <t>(RNA</t> read <t>count/DNA</t> read count). ( B, E ) Box plots displaying GC content for high and low activities cis- regulatory elements in U87 cells (B) and hNPCs (E). GC content is significantly different between high- and low-activity elements in both cell types ( P
    Zr Duet Rna Dna Miniprep Kit, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/zr duet rna dna miniprep kit/product/Zymo Research
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    zr duet rna dna miniprep kit - by Bioz Stars, 2019-12
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    GC content and dinucleotide composition are associated with regulatory activity in U87 cells and hNPCs. ( A, D ) Distributions of expression values for all cis- regulatory elements in U87 cells (A) and hNPCs (D). Expression values are averaged across the three biological replicates and plotted as log 2 (RNA read count/DNA read count). ( B, E ) Box plots displaying GC content for high and low activities cis- regulatory elements in U87 cells (B) and hNPCs (E). GC content is significantly different between high- and low-activity elements in both cell types ( P

    Journal: Nucleic Acids Research

    Article Title: A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells

    doi: 10.1093/nar/gkw942

    Figure Lengend Snippet: GC content and dinucleotide composition are associated with regulatory activity in U87 cells and hNPCs. ( A, D ) Distributions of expression values for all cis- regulatory elements in U87 cells (A) and hNPCs (D). Expression values are averaged across the three biological replicates and plotted as log 2 (RNA read count/DNA read count). ( B, E ) Box plots displaying GC content for high and low activities cis- regulatory elements in U87 cells (B) and hNPCs (E). GC content is significantly different between high- and low-activity elements in both cell types ( P

    Article Snippet: Total RNA was extracted from U87 cells and hNPCs 96 h after transduction using the ZR-Duet RNA/DNA MiniPrep kit (Zymo Research).

    Techniques: Gas Chromatography, Activity Assay, Expressing

    Quantitative LV-MPRA expression measurements are reproducible. ( A ) Putative cis -regulatory elements cloned upstream of an Hspa1b minimal promoter drive expression of dsRed containing DNA sequence barcodes in the 3΄ UTR. 2600 unique reporter gene constructs were cloned in parallel and the complex lentiviral plasmid library was used to produce lentivirus for transduction. U87 cells and human neural progenitor cells were transduced in triplicate and RNA/DNA were extracted after 96 h in culture. ( B ) Scatter plot showing expression measurements for cis -regulatory elements from two biological replicates in U87 cells. Expression in each replicate is plotted as log 2 (RNA read count/DNA read count). Correlation between expression values of regulatory elements with measurements for all five barcodes is 0.70. ( C ) Scatter plot from two biological replicates in human neural progenitor cells. Expression in each replicate is plotted as log 2 (RNA read count/DNA read count). Correlation between expression values of regulatory elements with measurements for all five barcodes is 0.63.

    Journal: Nucleic Acids Research

    Article Title: A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells

    doi: 10.1093/nar/gkw942

    Figure Lengend Snippet: Quantitative LV-MPRA expression measurements are reproducible. ( A ) Putative cis -regulatory elements cloned upstream of an Hspa1b minimal promoter drive expression of dsRed containing DNA sequence barcodes in the 3΄ UTR. 2600 unique reporter gene constructs were cloned in parallel and the complex lentiviral plasmid library was used to produce lentivirus for transduction. U87 cells and human neural progenitor cells were transduced in triplicate and RNA/DNA were extracted after 96 h in culture. ( B ) Scatter plot showing expression measurements for cis -regulatory elements from two biological replicates in U87 cells. Expression in each replicate is plotted as log 2 (RNA read count/DNA read count). Correlation between expression values of regulatory elements with measurements for all five barcodes is 0.70. ( C ) Scatter plot from two biological replicates in human neural progenitor cells. Expression in each replicate is plotted as log 2 (RNA read count/DNA read count). Correlation between expression values of regulatory elements with measurements for all five barcodes is 0.63.

    Article Snippet: Total RNA was extracted from U87 cells and hNPCs 96 h after transduction using the ZR-Duet RNA/DNA MiniPrep kit (Zymo Research).

    Techniques: Expressing, Clone Assay, Sequencing, Construct, Plasmid Preparation, Transduction

    Different DNA motifs are enriched in high expressing cis- regulatory elements in U87 cells and hNPCs. ( A ) Scatter plot showing average expression measurements for regulatory elements in U87 cells and hNPCs. Expression in each cell type is plotted as log 2 (RNA read count/DNA read count). Activity in the two cell types is significantly negatively correlated ( R = −0.326, P = 5.02e−53, Pearson's product-moment correlation). ( B ) AME analysis identified motifs enriched in regulatory elements with high activity in U87 cells relative to elements with high activity in hNPCs. ( C ) Motif enrichment in hNPC High Elements relative to U87 High Elements. Motifs enriched in U87 cells ( P

    Journal: Nucleic Acids Research

    Article Title: A genome-integrated massively parallel reporter assay reveals DNA sequence determinants of cis-regulatory activity in neural cells

    doi: 10.1093/nar/gkw942

    Figure Lengend Snippet: Different DNA motifs are enriched in high expressing cis- regulatory elements in U87 cells and hNPCs. ( A ) Scatter plot showing average expression measurements for regulatory elements in U87 cells and hNPCs. Expression in each cell type is plotted as log 2 (RNA read count/DNA read count). Activity in the two cell types is significantly negatively correlated ( R = −0.326, P = 5.02e−53, Pearson's product-moment correlation). ( B ) AME analysis identified motifs enriched in regulatory elements with high activity in U87 cells relative to elements with high activity in hNPCs. ( C ) Motif enrichment in hNPC High Elements relative to U87 High Elements. Motifs enriched in U87 cells ( P

    Article Snippet: Total RNA was extracted from U87 cells and hNPCs 96 h after transduction using the ZR-Duet RNA/DNA MiniPrep kit (Zymo Research).

    Techniques: Expressing, Activity Assay