monarch dna gel extraction kit  (New England Biolabs)


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    Name:
    Monarch DNA Gel Extraction Kit
    Description:
    Monarch DNA Gel Extraction Kit 250 preps
    Catalog Number:
    t1020l
    Price:
    466
    Size:
    250 preps
    Category:
    DNA Fragment Purification from Gels
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    New England Biolabs monarch dna gel extraction kit
    Monarch DNA Gel Extraction Kit
    Monarch DNA Gel Extraction Kit 250 preps
    https://www.bioz.com/result/monarch dna gel extraction kit/product/New England Biolabs
    Average 99 stars, based on 169 article reviews
    Price from $9.99 to $1999.99
    monarch dna gel extraction kit - by Bioz Stars, 2020-05
    99/100 stars

    Images

    1) Product Images from "Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior"

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2018.01569

    CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic DNA. Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) PCR evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.
    Figure Legend Snippet: CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic DNA. Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) PCR evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.

    Techniques Used: CRISPR, Introduce, Sequencing, Polymerase Chain Reaction, Amplification

    2) Product Images from "Proteogenomic Identification of a Novel Protein-Encoding Gene in Bovine Herpesvirus 1 That Is Expressed during Productive Infection"

    Article Title: Proteogenomic Identification of a Novel Protein-Encoding Gene in Bovine Herpesvirus 1 That Is Expressed during Productive Infection

    Journal: Viruses

    doi: 10.3390/v10090499

    Primer walking for elucidation of ORF-A 3′ terminus. Strand-specific RT-PCR of BoHV-1.1-infected cell mRNA extracts was was performed on cDNA produced from BoHV-1 infected cells using 16 different reverse primers that anneal further down (3′) to the viral genome. Successful amplification allowed for capture of increasing lengths of the ORF-A transcript sequence. RT indicates the presence (+) or absence (-) of a retrotranscriptase step with mRNA as a template. ( a ) Amplicons were produced with primers 1–8 using a 1-min extension time during PCR. ( b ) Amplicons were produced using primers 9-16 with a 2-min extension time to account for the increase in amplicon length.
    Figure Legend Snippet: Primer walking for elucidation of ORF-A 3′ terminus. Strand-specific RT-PCR of BoHV-1.1-infected cell mRNA extracts was was performed on cDNA produced from BoHV-1 infected cells using 16 different reverse primers that anneal further down (3′) to the viral genome. Successful amplification allowed for capture of increasing lengths of the ORF-A transcript sequence. RT indicates the presence (+) or absence (-) of a retrotranscriptase step with mRNA as a template. ( a ) Amplicons were produced with primers 1–8 using a 1-min extension time during PCR. ( b ) Amplicons were produced using primers 9-16 with a 2-min extension time to account for the increase in amplicon length.

    Techniques Used: Chromosome Walking, Reverse Transcription Polymerase Chain Reaction, Infection, Produced, Amplification, Sequencing, Polymerase Chain Reaction

    3) Product Images from "Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice"

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-23830-4

    Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii .
    Figure Legend Snippet: Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii .

    Techniques Used: Polymerase Chain Reaction, Amplification, Infection, Mouse Assay, Mass Spectrometry, Isolation, Cell Culture, Positive Control, Molecular Weight, Marker

    4) Product Images from "Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice"

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-23830-4

    Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii by PCR of faecal pellets, homogenized, and plated on selective agar plates. Number of colony forming units (CFU) is given per 100 mg of tissue. Individual data points shown; horizontal bar and whiskers indicate mean and standard error of the mean. Weight of tissue samples and CFU/organ are provided in Supplementary Table 1 .
    Figure Legend Snippet: Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii by PCR of faecal pellets, homogenized, and plated on selective agar plates. Number of colony forming units (CFU) is given per 100 mg of tissue. Individual data points shown; horizontal bar and whiskers indicate mean and standard error of the mean. Weight of tissue samples and CFU/organ are provided in Supplementary Table 1 .

    Techniques Used: Polymerase Chain Reaction, Amplification, Infection, Mouse Assay, Mass Spectrometry, Isolation, Cell Culture, Positive Control, Molecular Weight, Marker

    5) Product Images from "Evolution of a General RNA-Cleaving FANA Enzyme"

    Article Title: Evolution of a General RNA-Cleaving FANA Enzyme

    Journal: Nature Communications

    doi: 10.1038/s41467-018-07611-1

    FANA transcription and reverse transcription in vitro. a Constitutional structures for 2’-deoxyribonucleic acid (DNA) and 2’-fluoroarabino nucleic acid (FANA). b FANA transcription activity for wild-type archaeal DNA polymerases (exo−) from 9°N, DV, Kod, and Tgo (left panel). Samples were analyzed after 15 and 30 min at 55 °C. FANA reverse transcriptase activity of Bst DNA polymerase LF, 2.0, 3.0, and LF* (right panel). LF* denotes wild-type Bst DNA polymerase, large fragment, expressed and purified from E. coli . Samples were analyzed after 30 min at 50 °C. All samples were resolved on denaturing PAGE and visualized using a LI-COR Odyssey CLx. c Fidelity profile observed for FANA replication using Tgo and Bst LF* polymerases. The mutation profile reveals a mutation rate of 8 × 10 -4 and an overall fidelity of ~99.9%. d Catalytic rates observed for FANA synthesis with Tgo (left panel) and reverse transcription with Bst LF* (right panel)
    Figure Legend Snippet: FANA transcription and reverse transcription in vitro. a Constitutional structures for 2’-deoxyribonucleic acid (DNA) and 2’-fluoroarabino nucleic acid (FANA). b FANA transcription activity for wild-type archaeal DNA polymerases (exo−) from 9°N, DV, Kod, and Tgo (left panel). Samples were analyzed after 15 and 30 min at 55 °C. FANA reverse transcriptase activity of Bst DNA polymerase LF, 2.0, 3.0, and LF* (right panel). LF* denotes wild-type Bst DNA polymerase, large fragment, expressed and purified from E. coli . Samples were analyzed after 30 min at 50 °C. All samples were resolved on denaturing PAGE and visualized using a LI-COR Odyssey CLx. c Fidelity profile observed for FANA replication using Tgo and Bst LF* polymerases. The mutation profile reveals a mutation rate of 8 × 10 -4 and an overall fidelity of ~99.9%. d Catalytic rates observed for FANA synthesis with Tgo (left panel) and reverse transcription with Bst LF* (right panel)

    Techniques Used: In Vitro, Activity Assay, Purification, Polyacrylamide Gel Electrophoresis, Mutagenesis

    6) Product Images from "Evolution of a General RNA-Cleaving FANA Enzyme"

    Article Title: Evolution of a General RNA-Cleaving FANA Enzyme

    Journal: Nature Communications

    doi: 10.1038/s41467-018-07611-1

    FANA transcription and reverse transcription in vitro. a Constitutional structures for 2’-deoxyribonucleic acid (DNA) and 2’-fluoroarabino nucleic acid (FANA). b FANA transcription activity for wild-type archaeal DNA polymerases (exo−) from 9°N, DV, Kod, and Tgo (left panel). Samples were analyzed after 15 and 30 min at 55 °C. FANA reverse transcriptase activity of Bst DNA polymerase LF, 2.0, 3.0, and LF* (right panel). LF* denotes wild-type Bst DNA polymerase, large fragment, expressed and purified from E. coli . Samples were analyzed after 30 min at 50 °C. All samples were resolved on denaturing PAGE and visualized using a LI-COR Odyssey CLx. c Fidelity profile observed for FANA replication using Tgo and Bst LF* polymerases. The mutation profile reveals a mutation rate of 8 × 10 -4 and an overall fidelity of ~99.9%. d Catalytic rates observed for FANA synthesis with Tgo (left panel) and reverse transcription with Bst LF* (right panel)
    Figure Legend Snippet: FANA transcription and reverse transcription in vitro. a Constitutional structures for 2’-deoxyribonucleic acid (DNA) and 2’-fluoroarabino nucleic acid (FANA). b FANA transcription activity for wild-type archaeal DNA polymerases (exo−) from 9°N, DV, Kod, and Tgo (left panel). Samples were analyzed after 15 and 30 min at 55 °C. FANA reverse transcriptase activity of Bst DNA polymerase LF, 2.0, 3.0, and LF* (right panel). LF* denotes wild-type Bst DNA polymerase, large fragment, expressed and purified from E. coli . Samples were analyzed after 30 min at 50 °C. All samples were resolved on denaturing PAGE and visualized using a LI-COR Odyssey CLx. c Fidelity profile observed for FANA replication using Tgo and Bst LF* polymerases. The mutation profile reveals a mutation rate of 8 × 10 -4 and an overall fidelity of ~99.9%. d Catalytic rates observed for FANA synthesis with Tgo (left panel) and reverse transcription with Bst LF* (right panel)

    Techniques Used: In Vitro, Activity Assay, Purification, Polyacrylamide Gel Electrophoresis, Mutagenesis

    7) Product Images from "Effects of nuclear factor I phosphorylation on calpastatin (CAST) gene variant expression and subcellular distribution in malignant glioma cells"

    Article Title: Effects of nuclear factor I phosphorylation on calpastatin (CAST) gene variant expression and subcellular distribution in malignant glioma cells

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.RA118.004787

    CAST promoter activity and calpastatin isoform expression in MG cells. A , RLM RACE was carried out using 5 μg of total RNA isolated from NFI-hyperphosphorylated (T98) or NFI-hypophosphorylated (U251) MG cells. Antisense primer targeting exon 14 of the CAST gene was used for reverse transcription. Nested PCR amplification was carried out with 5′-ligated outer and inner primers and antisense primers targeting exons 8 and 4 of the CAST gene, respectively. PCR products were electrophoresed in 3% Metaphor (FMC Bioproducts) agarose gel, visualized with ethidium bromide, excised, purified, and sequenced using the BigDye Terminator version 3.1 cycle sequencing kit (Thermo Fisher Scientific). Exon composition of the isolated DNA products based on sequence analysis is indicated on the right. B , domain composition of XL-containing (full-length/type II) and XL-less (type III) calpastatin isoforms. T98 ( C ) and U251 ( D ) MG cells were transiently transfected with luciferase reporter constructs containing the CP (∼2000 bp upstream of CAST exon 1), ALT (in intron 3 containing the NFI-binding sites; ∼4000 bp upstream of CAST exon 4), or empty vector (CNT). Luciferase activity was measured using the Luciferase Assay System (Promega) and the FLUOstar microplate reader (BMG LABTECH). Relative -fold change was calculated relative to the empty vector control. Scatter plots show data from three independent experiments. E , U251 MG cells were transiently transfected with luciferase reporter constructs containing the WT ALT or constructs containing mutation at C2 (ALT-C2*), C3 (ALt-C3*), or both C2 and C3 (ALT-C2*C3*) NFI-binding sites. Luciferase activity was measured 48 h post-transfection as described above. p values were obtained from one-way analysis of variance statistical analysis of three independent experiments. *, p
    Figure Legend Snippet: CAST promoter activity and calpastatin isoform expression in MG cells. A , RLM RACE was carried out using 5 μg of total RNA isolated from NFI-hyperphosphorylated (T98) or NFI-hypophosphorylated (U251) MG cells. Antisense primer targeting exon 14 of the CAST gene was used for reverse transcription. Nested PCR amplification was carried out with 5′-ligated outer and inner primers and antisense primers targeting exons 8 and 4 of the CAST gene, respectively. PCR products were electrophoresed in 3% Metaphor (FMC Bioproducts) agarose gel, visualized with ethidium bromide, excised, purified, and sequenced using the BigDye Terminator version 3.1 cycle sequencing kit (Thermo Fisher Scientific). Exon composition of the isolated DNA products based on sequence analysis is indicated on the right. B , domain composition of XL-containing (full-length/type II) and XL-less (type III) calpastatin isoforms. T98 ( C ) and U251 ( D ) MG cells were transiently transfected with luciferase reporter constructs containing the CP (∼2000 bp upstream of CAST exon 1), ALT (in intron 3 containing the NFI-binding sites; ∼4000 bp upstream of CAST exon 4), or empty vector (CNT). Luciferase activity was measured using the Luciferase Assay System (Promega) and the FLUOstar microplate reader (BMG LABTECH). Relative -fold change was calculated relative to the empty vector control. Scatter plots show data from three independent experiments. E , U251 MG cells were transiently transfected with luciferase reporter constructs containing the WT ALT or constructs containing mutation at C2 (ALT-C2*), C3 (ALt-C3*), or both C2 and C3 (ALT-C2*C3*) NFI-binding sites. Luciferase activity was measured 48 h post-transfection as described above. p values were obtained from one-way analysis of variance statistical analysis of three independent experiments. *, p

    Techniques Used: Activity Assay, Expressing, Isolation, Nested PCR, Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Purification, Sequencing, Transfection, Luciferase, Construct, Binding Assay, Plasmid Preparation, Mutagenesis

    8) Product Images from "Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior"

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2018.01569

    CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic DNA. Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) PCR evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.
    Figure Legend Snippet: CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic DNA. Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) PCR evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.

    Techniques Used: CRISPR, Introduce, Sequencing, Polymerase Chain Reaction, Amplification

    9) Product Images from "Proteogenomic Identification of a Novel Protein-Encoding Gene in Bovine Herpesvirus 1 That Is Expressed during Productive Infection"

    Article Title: Proteogenomic Identification of a Novel Protein-Encoding Gene in Bovine Herpesvirus 1 That Is Expressed during Productive Infection

    Journal: Viruses

    doi: 10.3390/v10090499

    Primer walking for elucidation of ORF-A 3′ terminus. Strand-specific RT-PCR of BoHV-1.1-infected cell mRNA extracts was was performed on cDNA produced from BoHV-1 infected cells using 16 different reverse primers that anneal further down (3′) to the viral genome. Successful amplification allowed for capture of increasing lengths of the ORF-A transcript sequence. RT indicates the presence (+) or absence (-) of a retrotranscriptase step with mRNA as a template. ( a ) Amplicons were produced with primers 1–8 using a 1-min extension time during PCR. ( b ) Amplicons were produced using primers 9-16 with a 2-min extension time to account for the increase in amplicon length.
    Figure Legend Snippet: Primer walking for elucidation of ORF-A 3′ terminus. Strand-specific RT-PCR of BoHV-1.1-infected cell mRNA extracts was was performed on cDNA produced from BoHV-1 infected cells using 16 different reverse primers that anneal further down (3′) to the viral genome. Successful amplification allowed for capture of increasing lengths of the ORF-A transcript sequence. RT indicates the presence (+) or absence (-) of a retrotranscriptase step with mRNA as a template. ( a ) Amplicons were produced with primers 1–8 using a 1-min extension time during PCR. ( b ) Amplicons were produced using primers 9-16 with a 2-min extension time to account for the increase in amplicon length.

    Techniques Used: Chromosome Walking, Reverse Transcription Polymerase Chain Reaction, Infection, Produced, Amplification, Sequencing, Polymerase Chain Reaction

    Related Articles

    DNA Extraction:

    Article Title: Effects of nuclear factor I phosphorylation on calpastatin (CAST) gene variant expression and subcellular distribution in malignant glioma cells
    Article Snippet: .. The DNA was electrophoresed in a 3% MetaPhor agarose (FMC Bioproducts, Rockland, ME) gel, excised, purified (Monarch DNA extraction kit, New England Biolabs), and sequenced (BigDye Terminator® version 3.1 cycle sequencing kit, Thermo Fisher Scientific). .. The following reporter gene constructs were generated using the pGL3 luciferase vector (Promega) with the SV40 promoter element removed: (i) empty vector control (CNT), (ii) −1990 to +50 bp of the CAST promoter linked to the luciferase gene, with +1 denoting the first nucleotide of exon 1 (designated CP for canonical promoter region), and (iii) −4026 to +20 bp relative to exon 4, with +1 denoting the first nucleotide exon 4 (designated ALT for NFI-bound alternative promoter).

    Agarose Gel Electrophoresis:

    Article Title: Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany
    Article Snippet: .. PCR products were visualised on a 2% agarose gel, excised, and purified using a Monarch® DNA gel extraction kit (New England Biolabs, Ipswich, Massachusetts, United States). .. Purified products were then sent for Sanger sequencing using the applicable PCR primers.

    Purification:

    Article Title: Effects of nuclear factor I phosphorylation on calpastatin (CAST) gene variant expression and subcellular distribution in malignant glioma cells
    Article Snippet: .. The DNA was electrophoresed in a 3% MetaPhor agarose (FMC Bioproducts, Rockland, ME) gel, excised, purified (Monarch DNA extraction kit, New England Biolabs), and sequenced (BigDye Terminator® version 3.1 cycle sequencing kit, Thermo Fisher Scientific). .. The following reporter gene constructs were generated using the pGL3 luciferase vector (Promega) with the SV40 promoter element removed: (i) empty vector control (CNT), (ii) −1990 to +50 bp of the CAST promoter linked to the luciferase gene, with +1 denoting the first nucleotide of exon 1 (designated CP for canonical promoter region), and (iii) −4026 to +20 bp relative to exon 4, with +1 denoting the first nucleotide exon 4 (designated ALT for NFI-bound alternative promoter).

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior
    Article Snippet: .. All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively. ..

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer. .. Mice were sacrificed by cervical dislocation and the lungs were removed after ligation of the trachea to avoid alveolar collapse as described .

    Article Title: Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany
    Article Snippet: .. PCR products were visualised on a 2% agarose gel, excised, and purified using a Monarch® DNA gel extraction kit (New England Biolabs, Ipswich, Massachusetts, United States). .. Purified products were then sent for Sanger sequencing using the applicable PCR primers.

    Sequencing:

    Article Title: Effects of nuclear factor I phosphorylation on calpastatin (CAST) gene variant expression and subcellular distribution in malignant glioma cells
    Article Snippet: .. The DNA was electrophoresed in a 3% MetaPhor agarose (FMC Bioproducts, Rockland, ME) gel, excised, purified (Monarch DNA extraction kit, New England Biolabs), and sequenced (BigDye Terminator® version 3.1 cycle sequencing kit, Thermo Fisher Scientific). .. The following reporter gene constructs were generated using the pGL3 luciferase vector (Promega) with the SV40 promoter element removed: (i) empty vector control (CNT), (ii) −1990 to +50 bp of the CAST promoter linked to the luciferase gene, with +1 denoting the first nucleotide of exon 1 (designated CP for canonical promoter region), and (iii) −4026 to +20 bp relative to exon 4, with +1 denoting the first nucleotide exon 4 (designated ALT for NFI-bound alternative promoter).

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer. .. Mice were sacrificed by cervical dislocation and the lungs were removed after ligation of the trachea to avoid alveolar collapse as described .

    Polymerase Chain Reaction:

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior
    Article Snippet: .. All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively. ..

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer. .. Mice were sacrificed by cervical dislocation and the lungs were removed after ligation of the trachea to avoid alveolar collapse as described .

    Article Title: Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany
    Article Snippet: .. PCR products were visualised on a 2% agarose gel, excised, and purified using a Monarch® DNA gel extraction kit (New England Biolabs, Ipswich, Massachusetts, United States). .. Purified products were then sent for Sanger sequencing using the applicable PCR primers.

    Gel Extraction:

    Article Title: Evolution of a General RNA-Cleaving FANA Enzyme
    Article Snippet: .. ThermoPol buffer, Taq DNA polymerase, G. stearothermophilus Bst DNA polymerase, LF, and its variants Bst 2.0 DNA polymerase (2.0), and Bst 3.0 DNA polymerase (3.0), DH5α competent cells, and Monarch DNA gel extraction kits were purchased from New England Biolabs (Ipswich, MA). .. 3′–5′ exonuclease-deficient (exo−) archaeal polymerases isolated from Thermococcus sp. 9°N (9°N), Pyrococcus sp. deep vent (DV), T. gorgonarius (Tgo), T. kodakarensis (Kod), and G. stearothermophilus Bst DNA polymerase, LF* were expressed and purified from E. coli of the XL1-Blue strain from Agilent Technologies (Santa Clara, CA) as previously described .

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior
    Article Snippet: .. All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively. ..

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice
    Article Snippet: .. For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer. .. Mice were sacrificed by cervical dislocation and the lungs were removed after ligation of the trachea to avoid alveolar collapse as described .

    Article Title: Characterization of Equine Parvovirus in Thoroughbred Breeding Horses from Germany
    Article Snippet: .. PCR products were visualised on a 2% agarose gel, excised, and purified using a Monarch® DNA gel extraction kit (New England Biolabs, Ipswich, Massachusetts, United States). .. Purified products were then sent for Sanger sequencing using the applicable PCR primers.

    Article Title: Evolution of a General RNA-Cleaving FANA Enzyme
    Article Snippet: .. ThermoPol buffer, Taq DNA polymerase, G. stearothermophilus Bst DNA polymerase, LF, and its variants Bst 2.0 DNA polymerase (2.0), and Bst 3.0 DNA polymerase (3.0), DH5α competent cells, and Monarch DNA gel extraction kits were purchased from New England Biolabs (Ipswich, MA). .. 3′–5′ exonuclease-deficient (exo−) archaeal polymerases isolated from Thermococcus sp. 9°N (9°N), Pyrococcus sp. deep vent (DV), T. gorgonarius (Tgo), T. kodakarensis (Kod), and G. stearothermophilus Bst DNA polymerase, LF* were expressed and purified from E. coli of the XL1-Blue strain from Agilent Technologies (Santa Clara, CA) as previously described .

    Plasmid Preparation:

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior
    Article Snippet: .. All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively. ..

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    New England Biolabs monarch dna gel extraction kit
    CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic <t>DNA.</t> Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) <t>PCR</t> evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.
    Monarch Dna Gel Extraction Kit, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 93 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic DNA. Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) PCR evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.

    Journal: Frontiers in Microbiology

    Article Title: Efficient Genome Editing of Magnetospirillum magneticum AMB-1 by CRISPR-Cas9 System for Analyzing Magnetotactic Behavior

    doi: 10.3389/fmicb.2018.01569

    Figure Lengend Snippet: CRISPR-Cas9-assisted genome editing in M. magneticum AMB-1 cells. (A) Strategy for deletion of the amb0994 gene by CRISPR-Cas9 assisted HDR in M. magneticum AMB-1 cells. An sgRNA transcripts guide Cas9 nuclease to introduce DSBs at ends of amb0994 gene, while a codelivered editing template repairs the gap via HR. Kan is kanamycin. Gm is gentamycin. (B) Schematic of RNA-guided Cas9 nuclease uses for editing of the AMB-1 amb0994 . An sgRNA consisting of 20 nt sequence (black bar) guide the Cas9 nuclease (orange) to target and cleavage the genomic DNA. Cleavage sites are indicated by red arrows for ~3 bp upstream of PAM. (C,D) PCR evaluation of amb0994 deletion from five colonies (1–5) with WT control. (E) Six fragments within MAI were amplified to evaluate the maintenance of genomic MAI during deletion.

    Article Snippet: All PCR products and plasmids were purified using Monarch DNA Gel Extraction Kit (NEB, United States) and MiniBEST Plasmid Purification Kit (Takara, Japan), respectively.

    Techniques: CRISPR, Introduce, Sequencing, Polymerase Chain Reaction, Amplification

    Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii .

    Journal: Scientific Reports

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice

    doi: 10.1038/s41598-018-23830-4

    Figure Lengend Snippet: Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii .

    Article Snippet: For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer.

    Techniques: Polymerase Chain Reaction, Amplification, Infection, Mouse Assay, Mass Spectrometry, Isolation, Cell Culture, Positive Control, Molecular Weight, Marker

    Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii by PCR of faecal pellets, homogenized, and plated on selective agar plates. Number of colony forming units (CFU) is given per 100 mg of tissue. Individual data points shown; horizontal bar and whiskers indicate mean and standard error of the mean. Weight of tissue samples and CFU/organ are provided in Supplementary Table 1 .

    Journal: Scientific Reports

    Article Title: Bordetella pseudohinzii targets cilia and impairs tracheal cilia-driven transport in naturally acquired infection in mice

    doi: 10.1038/s41598-018-23830-4

    Figure Lengend Snippet: Detection of genomic Bordetella DNA by PCR. ( a ) A PCR product of 318 bp was amplified with B. pseudohinzii -specific primers from DNA of faeces (upper panel) and larynx (lower panel) from infected (lanes 1–4) and non-infected (lanes 5–8) mice, as classified by MALDI-TOF MS. DNA isolated from cultured B. pseudohinzii (strain 3227) served as a positive control (lane 9). Control runs without template were negative (lane 10). M: 100 bp molecular weight marker. ( b ) Trachea and lung taken were taken from 6 animals which were positive for B. pseudohinzii by PCR of faecal pellets, homogenized, and plated on selective agar plates. Number of colony forming units (CFU) is given per 100 mg of tissue. Individual data points shown; horizontal bar and whiskers indicate mean and standard error of the mean. Weight of tissue samples and CFU/organ are provided in Supplementary Table 1 .

    Article Snippet: For subsequent sequencing, PCR-products were purified by the use of the Monarch DNA Gel Extraction Kit (New England Biolabs, Frankfurt, Germany) as recommended by the manufacturer.

    Techniques: Polymerase Chain Reaction, Amplification, Infection, Mouse Assay, Mass Spectrometry, Isolation, Cell Culture, Positive Control, Molecular Weight, Marker

    FANA transcription and reverse transcription in vitro. a Constitutional structures for 2’-deoxyribonucleic acid (DNA) and 2’-fluoroarabino nucleic acid (FANA). b FANA transcription activity for wild-type archaeal DNA polymerases (exo−) from 9°N, DV, Kod, and Tgo (left panel). Samples were analyzed after 15 and 30 min at 55 °C. FANA reverse transcriptase activity of Bst DNA polymerase LF, 2.0, 3.0, and LF* (right panel). LF* denotes wild-type Bst DNA polymerase, large fragment, expressed and purified from E. coli . Samples were analyzed after 30 min at 50 °C. All samples were resolved on denaturing PAGE and visualized using a LI-COR Odyssey CLx. c Fidelity profile observed for FANA replication using Tgo and Bst LF* polymerases. The mutation profile reveals a mutation rate of 8 × 10 -4 and an overall fidelity of ~99.9%. d Catalytic rates observed for FANA synthesis with Tgo (left panel) and reverse transcription with Bst LF* (right panel)

    Journal: Nature Communications

    Article Title: Evolution of a General RNA-Cleaving FANA Enzyme

    doi: 10.1038/s41467-018-07611-1

    Figure Lengend Snippet: FANA transcription and reverse transcription in vitro. a Constitutional structures for 2’-deoxyribonucleic acid (DNA) and 2’-fluoroarabino nucleic acid (FANA). b FANA transcription activity for wild-type archaeal DNA polymerases (exo−) from 9°N, DV, Kod, and Tgo (left panel). Samples were analyzed after 15 and 30 min at 55 °C. FANA reverse transcriptase activity of Bst DNA polymerase LF, 2.0, 3.0, and LF* (right panel). LF* denotes wild-type Bst DNA polymerase, large fragment, expressed and purified from E. coli . Samples were analyzed after 30 min at 50 °C. All samples were resolved on denaturing PAGE and visualized using a LI-COR Odyssey CLx. c Fidelity profile observed for FANA replication using Tgo and Bst LF* polymerases. The mutation profile reveals a mutation rate of 8 × 10 -4 and an overall fidelity of ~99.9%. d Catalytic rates observed for FANA synthesis with Tgo (left panel) and reverse transcription with Bst LF* (right panel)

    Article Snippet: ThermoPol buffer, Taq DNA polymerase, G. stearothermophilus Bst DNA polymerase, LF, and its variants Bst 2.0 DNA polymerase (2.0), and Bst 3.0 DNA polymerase (3.0), DH5α competent cells, and Monarch DNA gel extraction kits were purchased from New England Biolabs (Ipswich, MA).

    Techniques: In Vitro, Activity Assay, Purification, Polyacrylamide Gel Electrophoresis, Mutagenesis