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    New England Biolabs λ exonuclease reaction buffer
    ChIP-exo 5.0 increases library yield. a Schematic of ChIP-exo 5.0. The purple triangle indicates the location of the Read_1 start site, which is also the <t>λ</t> exonuclease stop site. b 2% agarose gel of the electrophoresed library following 18 cycles of PCR for various S. cerevisiae transcription factors assayed by ChIP-exo 1.1 or 5.0. Following ChIP, the sample was split and libraries prepared using the indicated protocols. After splitting the sample, each reaction contained a 50 ml cell equivalent (OD 600 = 0.8) of yeast chromatin, which is five-fold less than the amount optimized for ChIP-exo 1.1. ChIP-exo 5.0 produced greater library yield for all samples. c Heatmaps comparing ChIP-exo 1.1 and 5.0 at the 975 Reb1 primary motifs in a 200 bp window. d Composite plot of data from panel ( c )
    λ Exonuclease Reaction Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/λ exonuclease reaction buffer/product/New England Biolabs
    Average 99 stars, based on 30 article reviews
    Price from $9.99 to $1999.99
    λ exonuclease reaction buffer - by Bioz Stars, 2020-08
    99/100 stars
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    99
    Thermo Fisher λ exonuclease reaction buffer
    ChIP-exo 5.0 increases library yield. a Schematic of ChIP-exo 5.0. The purple triangle indicates the location of the Read_1 start site, which is also the <t>λ</t> exonuclease stop site. b 2% agarose gel of the electrophoresed library following 18 cycles of PCR for various S. cerevisiae transcription factors assayed by ChIP-exo 1.1 or 5.0. Following ChIP, the sample was split and libraries prepared using the indicated protocols. After splitting the sample, each reaction contained a 50 ml cell equivalent (OD 600 = 0.8) of yeast chromatin, which is five-fold less than the amount optimized for ChIP-exo 1.1. ChIP-exo 5.0 produced greater library yield for all samples. c Heatmaps comparing ChIP-exo 1.1 and 5.0 at the 975 Reb1 primary motifs in a 200 bp window. d Composite plot of data from panel ( c )
    λ Exonuclease Reaction Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/λ exonuclease reaction buffer/product/Thermo Fisher
    Average 99 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    λ exonuclease reaction buffer - by Bioz Stars, 2020-08
    99/100 stars
      Buy from Supplier

    95
    Thermo Fisher λ exonuclease buffer
    ChIP-exo 5.0 increases library yield. a Schematic of ChIP-exo 5.0. The purple triangle indicates the location of the Read_1 start site, which is also the <t>λ</t> exonuclease stop site. b 2% agarose gel of the electrophoresed library following 18 cycles of PCR for various S. cerevisiae transcription factors assayed by ChIP-exo 1.1 or 5.0. Following ChIP, the sample was split and libraries prepared using the indicated protocols. After splitting the sample, each reaction contained a 50 ml cell equivalent (OD 600 = 0.8) of yeast chromatin, which is five-fold less than the amount optimized for ChIP-exo 1.1. ChIP-exo 5.0 produced greater library yield for all samples. c Heatmaps comparing ChIP-exo 1.1 and 5.0 at the 975 Reb1 primary motifs in a 200 bp window. d Composite plot of data from panel ( c )
    λ Exonuclease Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/λ exonuclease buffer/product/Thermo Fisher
    Average 95 stars, based on 7 article reviews
    Price from $9.99 to $1999.99
    λ exonuclease buffer - by Bioz Stars, 2020-08
    95/100 stars
      Buy from Supplier

    Image Search Results


    ChIP-exo 5.0 increases library yield. a Schematic of ChIP-exo 5.0. The purple triangle indicates the location of the Read_1 start site, which is also the λ exonuclease stop site. b 2% agarose gel of the electrophoresed library following 18 cycles of PCR for various S. cerevisiae transcription factors assayed by ChIP-exo 1.1 or 5.0. Following ChIP, the sample was split and libraries prepared using the indicated protocols. After splitting the sample, each reaction contained a 50 ml cell equivalent (OD 600 = 0.8) of yeast chromatin, which is five-fold less than the amount optimized for ChIP-exo 1.1. ChIP-exo 5.0 produced greater library yield for all samples. c Heatmaps comparing ChIP-exo 1.1 and 5.0 at the 975 Reb1 primary motifs in a 200 bp window. d Composite plot of data from panel ( c )

    Journal: Nature Communications

    Article Title: Simplified ChIP-exo assays

    doi: 10.1038/s41467-018-05265-7

    Figure Lengend Snippet: ChIP-exo 5.0 increases library yield. a Schematic of ChIP-exo 5.0. The purple triangle indicates the location of the Read_1 start site, which is also the λ exonuclease stop site. b 2% agarose gel of the electrophoresed library following 18 cycles of PCR for various S. cerevisiae transcription factors assayed by ChIP-exo 1.1 or 5.0. Following ChIP, the sample was split and libraries prepared using the indicated protocols. After splitting the sample, each reaction contained a 50 ml cell equivalent (OD 600 = 0.8) of yeast chromatin, which is five-fold less than the amount optimized for ChIP-exo 1.1. ChIP-exo 5.0 produced greater library yield for all samples. c Heatmaps comparing ChIP-exo 1.1 and 5.0 at the 975 Reb1 primary motifs in a 200 bp window. d Composite plot of data from panel ( c )

    Article Snippet: The λ exonuclease digestion (100 µl) containing: 20 U λ exonuclease (NEB), 1 × λ exonuclease reaction buffer (NEB), 0.1% Triton-X 100, and 5% DMSO was incubated for 30 min at 37 °C; then washed with 10 mM Tris-HCl, pH 8.0 at 4 °C.

    Techniques: Chromatin Immunoprecipitation, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Produced

    Overproduction of Din7 enhances 5′−3′ dsDNA exonuclease activity in mitochondria. ( A ) Principle of the 5′−3′ and 3′−5′ exonuclease activity assay. The 5′- and 3′- 32 P-labels were preferentially removed by 5′−3′ and 3′−5′ exonuclease activity, and they are resistant to 3′−5′ and 5′−3′ exonucleases, respectively. ( B ) Schematic diagram of the construction of the Din7 deletion mutant (Din7Δ). Immunoblot analysis of overproduced C-terminally 6× His-tagged Din7 or Din7Δ in mitochondrial extracts (bottom). Mitochondria were isolated from cells bearing WT/pYES2/CT, WT/pYES2/CT-DIN7 and WT/pYES2/CT-din7Δ (overproducing Din7Δ with a C-terminal 6× His tag). The signals of overproduced Din7 and Din7Δ were detected using a monoclonal anti-6× His-tag antibody. As a control, the levels of porin (a constitutively expressed protein, used here as a control) were determined by immunoblot analysis using a monoclonal anti-porin antibody to adjust the protein concentrations of mitochondrial extracts from all three strains to the same level. ( C and E ) Analyses of 5′−3′ or 3′−5′ exonuclease activity in mitochondrial extracts. The 5′- or 3′- 32 P-labeled pUC119/HincII dsDNA fragments were incubated at 37°C for 15 min with increasing concentrations of mitochondrial extracts. After removing the proteins by treating the extracts with proteinase K, the DNA molecules were separated on a 1% agarose gel. ( D and F ) Quantitative representation of the 5′−3′ and 3′−5′ exonuclease activities in mitochondrial extracts, detected in (C) and (E). Signals relative to untreated DNA are plotted. ds, double-stranded; ss, single-stranded. Open circles, incubated with mitochondrial extracts from wild-type cells (cells without Din7 overproduction); closed circles, incubated with mitochondrial extracts from Din7-overproducing cells; closed triangles, incubated with mitochondrial extracts from Din7Δ-overproducing cells. Each bar represents the results of at least two independent experiments. ( G ) The generation of single-stranded DNA by Din7. HincII-linearized pUC119 DNA (104 µM) was treated at 37°C for 5 min with increasing amounts of mitochondrial extracts derived from cells of WT/pYES2/CT, WT/pYES2/CT-DIN7 or WT/pYES2/CT-din7Δ in the same buffer used for detection of λ exonuclease activity. Then, each reaction solution (10 µl) was separated into duplicate aliquots. Proteinase K was added to one aliquot to stop the reaction. The second aliquot from each set was treated at 37°C for 10 min with 2.25 U mung bean nuclease followed by addition of proteinase K to stop the reaction. Mung bean nuclease digests only the single-stranded DNA, leaving the double-stranded DNA intact. Samples were then electrophoresed on a 1% agarose gel and stained with ethidium bromide. Lane 1, 1-kb plus ladder used as a size marker; lane 2, HincII-linearized pUC119 DNA; lane 3, HincII-linearized pUC119 DNA treated in a reaction mixture without mitochondrial extracts; lanes 4–7, HincII-linearized pUC119 DNA treated with increasing amounts of mitochondrial extracts; lane 8, HincII-linearized pUC119 DNA treated only with mung bean nuclease; lanes 9–12, samples treated as in lanes 4–7, treated additionally with mung bean nuclease. The samples treated with mitochondrial extracts overexpressing DIN7 contain both single-stranded DNA fragments with discrete sizes and double-stranded DNA because discrete DNA signals smaller than those of the double-stranded DNA in the middle were removed by mung bean nuclease treatments.

    Journal: Nucleic Acids Research

    Article Title: Din7 and Mhr1 expression levels regulate double-strand-break-induced replication and recombination of mtDNA at ori5 in yeast

    doi: 10.1093/nar/gkt273

    Figure Lengend Snippet: Overproduction of Din7 enhances 5′−3′ dsDNA exonuclease activity in mitochondria. ( A ) Principle of the 5′−3′ and 3′−5′ exonuclease activity assay. The 5′- and 3′- 32 P-labels were preferentially removed by 5′−3′ and 3′−5′ exonuclease activity, and they are resistant to 3′−5′ and 5′−3′ exonucleases, respectively. ( B ) Schematic diagram of the construction of the Din7 deletion mutant (Din7Δ). Immunoblot analysis of overproduced C-terminally 6× His-tagged Din7 or Din7Δ in mitochondrial extracts (bottom). Mitochondria were isolated from cells bearing WT/pYES2/CT, WT/pYES2/CT-DIN7 and WT/pYES2/CT-din7Δ (overproducing Din7Δ with a C-terminal 6× His tag). The signals of overproduced Din7 and Din7Δ were detected using a monoclonal anti-6× His-tag antibody. As a control, the levels of porin (a constitutively expressed protein, used here as a control) were determined by immunoblot analysis using a monoclonal anti-porin antibody to adjust the protein concentrations of mitochondrial extracts from all three strains to the same level. ( C and E ) Analyses of 5′−3′ or 3′−5′ exonuclease activity in mitochondrial extracts. The 5′- or 3′- 32 P-labeled pUC119/HincII dsDNA fragments were incubated at 37°C for 15 min with increasing concentrations of mitochondrial extracts. After removing the proteins by treating the extracts with proteinase K, the DNA molecules were separated on a 1% agarose gel. ( D and F ) Quantitative representation of the 5′−3′ and 3′−5′ exonuclease activities in mitochondrial extracts, detected in (C) and (E). Signals relative to untreated DNA are plotted. ds, double-stranded; ss, single-stranded. Open circles, incubated with mitochondrial extracts from wild-type cells (cells without Din7 overproduction); closed circles, incubated with mitochondrial extracts from Din7-overproducing cells; closed triangles, incubated with mitochondrial extracts from Din7Δ-overproducing cells. Each bar represents the results of at least two independent experiments. ( G ) The generation of single-stranded DNA by Din7. HincII-linearized pUC119 DNA (104 µM) was treated at 37°C for 5 min with increasing amounts of mitochondrial extracts derived from cells of WT/pYES2/CT, WT/pYES2/CT-DIN7 or WT/pYES2/CT-din7Δ in the same buffer used for detection of λ exonuclease activity. Then, each reaction solution (10 µl) was separated into duplicate aliquots. Proteinase K was added to one aliquot to stop the reaction. The second aliquot from each set was treated at 37°C for 10 min with 2.25 U mung bean nuclease followed by addition of proteinase K to stop the reaction. Mung bean nuclease digests only the single-stranded DNA, leaving the double-stranded DNA intact. Samples were then electrophoresed on a 1% agarose gel and stained with ethidium bromide. Lane 1, 1-kb plus ladder used as a size marker; lane 2, HincII-linearized pUC119 DNA; lane 3, HincII-linearized pUC119 DNA treated in a reaction mixture without mitochondrial extracts; lanes 4–7, HincII-linearized pUC119 DNA treated with increasing amounts of mitochondrial extracts; lane 8, HincII-linearized pUC119 DNA treated only with mung bean nuclease; lanes 9–12, samples treated as in lanes 4–7, treated additionally with mung bean nuclease. The samples treated with mitochondrial extracts overexpressing DIN7 contain both single-stranded DNA fragments with discrete sizes and double-stranded DNA because discrete DNA signals smaller than those of the double-stranded DNA in the middle were removed by mung bean nuclease treatments.

    Article Snippet: Assay for exonuclease activities in mitochondria The 5′-labeled pUC119/HincII dsDNA fragments (75 nM) and the 3′-labeled pUC119/BamHI dsDNA fragments (87 nM) were incubated at 37°C for 15 min with various amounts (0, 4, 20, 32 and 50 µg/ml in protein) of mitochondrial extracts in a 10-µl reaction solution containing 1× λ exonuclease buffer (New England BioLabs Inc., MA, USA): 67 mM glycine–KOH (pH 9.4), 2.5 mM MgCl2 and 50 µg/ml of bovine serum albumin.

    Techniques: Activity Assay, Mutagenesis, Isolation, Labeling, Incubation, Agarose Gel Electrophoresis, Derivative Assay, Staining, Marker