dna polymerases  (New England Biolabs)


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    Structured Review

    New England Biolabs dna polymerases
    Dna Polymerases, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/dna polymerases/product/New England Biolabs
    Average 95 stars, based on 20 article reviews
    Price from $9.99 to $1999.99
    dna polymerases - by Bioz Stars, 2020-04
    95/100 stars

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    Related Articles

    Clone Assay:

    Article Title: Construction of an infectious cDNA clone of Enterovirus 71: insights into the factors ensuring experimental success.
    Article Snippet: In contrast to the overlapping PCR, the long distance PCR approach required optimization of PCR conditions in order to obtain sufficient amounts of DNA from a single round for downstream analyses, gel purification and cloning. .. Additionally, a number of DNA polymerases recommended for long template amplification were used unsuccessfully (LongAmp TM Taq from New England Bio-Labs, Ipswich, MA, USA; Expand Long Template PCR System from Roche Applied Science, Upper Bavaria, Germany; and an in-house mix of Pfu DNA Pol and GoTaq ® DNA Pol which were supplied from Promega, Madison, WI, USA) prior to obtaining positive results with iProof High-Fidelity DNA Pol.

    Amplification:

    Article Title: Construction of an infectious cDNA clone of Enterovirus 71: insights into the factors ensuring experimental success.
    Article Snippet: .. Additionally, a number of DNA polymerases recommended for long template amplification were used unsuccessfully (LongAmp TM Taq from New England Bio-Labs, Ipswich, MA, USA; Expand Long Template PCR System from Roche Applied Science, Upper Bavaria, Germany; and an in-house mix of Pfu DNA Pol and GoTaq ® DNA Pol which were supplied from Promega, Madison, WI, USA) prior to obtaining positive results with iProof High-Fidelity DNA Pol. .. When performed under conditions described above (Section 2.3.2), the long-PCR amplification resulted in an adequate yield of the PCR product of expected length, and with no additional non-specific bands observed by agarose gel electrophoresis (Fig. 1B) .

    Agarose Gel Electrophoresis:

    Article Title: Construction of an infectious cDNA clone of Enterovirus 71: insights into the factors ensuring experimental success.
    Article Snippet: Additionally, a number of DNA polymerases recommended for long template amplification were used unsuccessfully (LongAmp TM Taq from New England Bio-Labs, Ipswich, MA, USA; Expand Long Template PCR System from Roche Applied Science, Upper Bavaria, Germany; and an in-house mix of Pfu DNA Pol and GoTaq ® DNA Pol which were supplied from Promega, Madison, WI, USA) prior to obtaining positive results with iProof High-Fidelity DNA Pol. .. When performed under conditions described above (Section 2.3.2), the long-PCR amplification resulted in an adequate yield of the PCR product of expected length, and with no additional non-specific bands observed by agarose gel electrophoresis (Fig. 1B) .

    Produced:

    Article Title: Construction of an infectious cDNA clone of Enterovirus 71: insights into the factors ensuring experimental success.
    Article Snippet: In the first round of the overlapping PCR the 5 half of the EV 71 genome was produced at a lower amount compared to the 3 fragment (data not shown). .. Additionally, a number of DNA polymerases recommended for long template amplification were used unsuccessfully (LongAmp TM Taq from New England Bio-Labs, Ipswich, MA, USA; Expand Long Template PCR System from Roche Applied Science, Upper Bavaria, Germany; and an in-house mix of Pfu DNA Pol and GoTaq ® DNA Pol which were supplied from Promega, Madison, WI, USA) prior to obtaining positive results with iProof High-Fidelity DNA Pol.

    Polymerase Chain Reaction:

    Article Title: Construction of an infectious cDNA clone of Enterovirus 71: insights into the factors ensuring experimental success.
    Article Snippet: .. Additionally, a number of DNA polymerases recommended for long template amplification were used unsuccessfully (LongAmp TM Taq from New England Bio-Labs, Ipswich, MA, USA; Expand Long Template PCR System from Roche Applied Science, Upper Bavaria, Germany; and an in-house mix of Pfu DNA Pol and GoTaq ® DNA Pol which were supplied from Promega, Madison, WI, USA) prior to obtaining positive results with iProof High-Fidelity DNA Pol. .. When performed under conditions described above (Section 2.3.2), the long-PCR amplification resulted in an adequate yield of the PCR product of expected length, and with no additional non-specific bands observed by agarose gel electrophoresis (Fig. 1B) .

    Gel Purification:

    Article Title: Construction of an infectious cDNA clone of Enterovirus 71: insights into the factors ensuring experimental success.
    Article Snippet: In contrast to the overlapping PCR, the long distance PCR approach required optimization of PCR conditions in order to obtain sufficient amounts of DNA from a single round for downstream analyses, gel purification and cloning. .. Additionally, a number of DNA polymerases recommended for long template amplification were used unsuccessfully (LongAmp TM Taq from New England Bio-Labs, Ipswich, MA, USA; Expand Long Template PCR System from Roche Applied Science, Upper Bavaria, Germany; and an in-house mix of Pfu DNA Pol and GoTaq ® DNA Pol which were supplied from Promega, Madison, WI, USA) prior to obtaining positive results with iProof High-Fidelity DNA Pol.

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    OneTaq Quick Load DNA Polymerase 500 units
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    New England Biolabs exdna
    Agarose gel of PCRs from ϕSa4ms selective-depletion experiment. One percent agarose gel stained with SYBR Safe <t>DNA</t> Gel Stain containing end-point PCRs from MSSA476 samples. MSSA476 <t>exDNA</t> was digested with Plasmid-safe exonuclease, Psh AI/ Psp XI restriction endonucleases, both Plasmid-safe and restriction endonuclease, or left untreated with treatment indicated by “+” and “–”. Gapdh , ϕSa3ms attP , ϕSa4ms attP , and pSAS1 target were amplified from treated and untreated samples. ϕSa4ms attP target is selectively depleted from combination exonuclease and endonuclease treatment but not solely exonuclease treatment, indicating its existence as a circular element in exDNA samples. Higher levels of ϕSa4ms target compared to ϕSa3ms target correlate with phage enrichment in sequencing. Negative controls for each primer set are shown. The 500 bp ladder band is indicated.
    Exdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs dna methylation treatment
    mtDNA methylation identified by pyro-sequencing. Levels of <t>DNA</t> methylation at <t>CpG</t> sites in a HSP, b LSP, and c ND6 regions of 143B cells, 143B 143B early and 143B 143B late tumors were determined by pyro-sequencing. Statistical significance was determined by One-way ANOVA. Bars represent the mean of the percentage of DNA methylation (mean ± SEM; n = 3). * and ** indicate p values of
    Dna Methylation Treatment, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs methyltransferase buffer
    Single-Molecule Detection of CMG Pausing at a Lagging-Strand <t>Methyltransferase</t> Block (A) Schematic representation of experimental approach used in single-molecule DNA unwinding assays. (B) Images of a sample field of view showing accumulation of EGFP-RPA fluorescence signal at different time points from the addition of EGFP-RPA into the chamber. (C) Example unwinding traces of DNA substrates without a protein barrier. Traces exhibit a signal drop upon completion of unwinding due to dissociation of the leading-strand template (depicted in A). (D) Distribution of average fork rates measured in fully unwound substrates without MH (black) and after bypassing MH Lag (blue). Number of molecules are n(-MH) = 199, n(MH Lag after pause) = 20. (E) Sample unwinding traces of DNA substrates modified with MH Lag . Pausing observed at 800 bp is highlighted with gray rectangle. (F) Distribution of pause durations observed in molecules exhibiting a pausing event (n = 109). The solid line is a fit to a single exponential. See also Figure S6 .
    Methyltransferase Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/methyltransferase buffer/product/New England Biolabs
    Average 96 stars, based on 4 article reviews
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    Agarose gel of PCRs from ϕSa4ms selective-depletion experiment. One percent agarose gel stained with SYBR Safe DNA Gel Stain containing end-point PCRs from MSSA476 samples. MSSA476 exDNA was digested with Plasmid-safe exonuclease, Psh AI/ Psp XI restriction endonucleases, both Plasmid-safe and restriction endonuclease, or left untreated with treatment indicated by “+” and “–”. Gapdh , ϕSa3ms attP , ϕSa4ms attP , and pSAS1 target were amplified from treated and untreated samples. ϕSa4ms attP target is selectively depleted from combination exonuclease and endonuclease treatment but not solely exonuclease treatment, indicating its existence as a circular element in exDNA samples. Higher levels of ϕSa4ms target compared to ϕSa3ms target correlate with phage enrichment in sequencing. Negative controls for each primer set are shown. The 500 bp ladder band is indicated.

    Journal: Frontiers in Microbiology

    Article Title: Extra-Chromosomal DNA Sequencing Reveals Episomal Prophages Capable of Impacting Virulence Factor Expression in Staphylococcus aureus

    doi: 10.3389/fmicb.2018.01406

    Figure Lengend Snippet: Agarose gel of PCRs from ϕSa4ms selective-depletion experiment. One percent agarose gel stained with SYBR Safe DNA Gel Stain containing end-point PCRs from MSSA476 samples. MSSA476 exDNA was digested with Plasmid-safe exonuclease, Psh AI/ Psp XI restriction endonucleases, both Plasmid-safe and restriction endonuclease, or left untreated with treatment indicated by “+” and “–”. Gapdh , ϕSa3ms attP , ϕSa4ms attP , and pSAS1 target were amplified from treated and untreated samples. ϕSa4ms attP target is selectively depleted from combination exonuclease and endonuclease treatment but not solely exonuclease treatment, indicating its existence as a circular element in exDNA samples. Higher levels of ϕSa4ms target compared to ϕSa3ms target correlate with phage enrichment in sequencing. Negative controls for each primer set are shown. The 500 bp ladder band is indicated.

    Article Snippet: Linear DNase and Restriction Endonuclease Treatment of exDNA Samples and End-Point PCR of DNA Targets Prior to linear DNase and/or treatment with restriction endonuclease, exDNA samples were treated with PreCR Repair Mix (NEB) to repair nicked DNA.

    Techniques: Agarose Gel Electrophoresis, Staining, Plasmid Preparation, Amplification, Sequencing

    Read mapping and coverage analysis of MSSA476 extra-chromosomal DNA sequencing. (A,B) Read mappings of sequencing reads for MSSA476 exDNA. ϕSa4ms (B) has greater read coverage compared to ϕSa3ms (A) in exDNA sequencing. Selected portions of the read mapping surrounding prophage integration sites for ϕSa3ms (A) and ϕSa4ms (B) are shown. Chromosomal positions are labeled at top, and consensus regions are shown below for MSSA476 chromosome sequence and MSSA476 exDNA reads. Locations of ϕSa3ms (A) and ϕSa4ms (B) integrated prophage genomes are shown. Extra-chromosomal reads are shown below for each. (C) Coverage analysis histogram from MSSA476 extra-chromosomal DNA sequencing read mapping. Portions of coverage analysis histogram surrounding prophage regions shown for clarity. Chromosomal positions labeled at top of image, and approximate positions of ϕSa3ms and ϕSa4ms genomes shown below. Histogram of higher read-coverage regions on the MSSA476 chromosome contains 11 significantly higher coverage regions within the ϕSa4ms prophage genome location, indicating prophage enrichment in exDNA sequencing. Read-mapping across ϕSa3ms prophage genome location does not contain any regions of significantly higher coverage, indicating no prophage enrichment by exDNA isolation and sequencing.

    Journal: Frontiers in Microbiology

    Article Title: Extra-Chromosomal DNA Sequencing Reveals Episomal Prophages Capable of Impacting Virulence Factor Expression in Staphylococcus aureus

    doi: 10.3389/fmicb.2018.01406

    Figure Lengend Snippet: Read mapping and coverage analysis of MSSA476 extra-chromosomal DNA sequencing. (A,B) Read mappings of sequencing reads for MSSA476 exDNA. ϕSa4ms (B) has greater read coverage compared to ϕSa3ms (A) in exDNA sequencing. Selected portions of the read mapping surrounding prophage integration sites for ϕSa3ms (A) and ϕSa4ms (B) are shown. Chromosomal positions are labeled at top, and consensus regions are shown below for MSSA476 chromosome sequence and MSSA476 exDNA reads. Locations of ϕSa3ms (A) and ϕSa4ms (B) integrated prophage genomes are shown. Extra-chromosomal reads are shown below for each. (C) Coverage analysis histogram from MSSA476 extra-chromosomal DNA sequencing read mapping. Portions of coverage analysis histogram surrounding prophage regions shown for clarity. Chromosomal positions labeled at top of image, and approximate positions of ϕSa3ms and ϕSa4ms genomes shown below. Histogram of higher read-coverage regions on the MSSA476 chromosome contains 11 significantly higher coverage regions within the ϕSa4ms prophage genome location, indicating prophage enrichment in exDNA sequencing. Read-mapping across ϕSa3ms prophage genome location does not contain any regions of significantly higher coverage, indicating no prophage enrichment by exDNA isolation and sequencing.

    Article Snippet: Linear DNase and Restriction Endonuclease Treatment of exDNA Samples and End-Point PCR of DNA Targets Prior to linear DNase and/or treatment with restriction endonuclease, exDNA samples were treated with PreCR Repair Mix (NEB) to repair nicked DNA.

    Techniques: DNA Sequencing, Sequencing, Labeling, Isolation

    mtDNA methylation identified by pyro-sequencing. Levels of DNA methylation at CpG sites in a HSP, b LSP, and c ND6 regions of 143B cells, 143B 143B early and 143B 143B late tumors were determined by pyro-sequencing. Statistical significance was determined by One-way ANOVA. Bars represent the mean of the percentage of DNA methylation (mean ± SEM; n = 3). * and ** indicate p values of

    Journal: Clinical Epigenetics

    Article Title: The degree of mitochondrial DNA methylation in tumor models of glioblastoma and osteosarcoma

    doi: 10.1186/s13148-018-0590-0

    Figure Lengend Snippet: mtDNA methylation identified by pyro-sequencing. Levels of DNA methylation at CpG sites in a HSP, b LSP, and c ND6 regions of 143B cells, 143B 143B early and 143B 143B late tumors were determined by pyro-sequencing. Statistical significance was determined by One-way ANOVA. Bars represent the mean of the percentage of DNA methylation (mean ± SEM; n = 3). * and ** indicate p values of

    Article Snippet: Similarly, the positive controls comprised the two long PCR products that had been combined and underwent DNA methylation treatment using an in vitro CpG methyltransferase, M.SssI (New England Biolabs, MA, USA), according to the manufacturer’s instructions.

    Techniques: Methylation, Sequencing, DNA Methylation Assay

    Single-Molecule Detection of CMG Pausing at a Lagging-Strand Methyltransferase Block (A) Schematic representation of experimental approach used in single-molecule DNA unwinding assays. (B) Images of a sample field of view showing accumulation of EGFP-RPA fluorescence signal at different time points from the addition of EGFP-RPA into the chamber. (C) Example unwinding traces of DNA substrates without a protein barrier. Traces exhibit a signal drop upon completion of unwinding due to dissociation of the leading-strand template (depicted in A). (D) Distribution of average fork rates measured in fully unwound substrates without MH (black) and after bypassing MH Lag (blue). Number of molecules are n(-MH) = 199, n(MH Lag after pause) = 20. (E) Sample unwinding traces of DNA substrates modified with MH Lag . Pausing observed at 800 bp is highlighted with gray rectangle. (F) Distribution of pause durations observed in molecules exhibiting a pausing event (n = 109). The solid line is a fit to a single exponential. See also Figure S6 .

    Journal: Cell Reports

    Article Title: Dynamics of the Eukaryotic Replicative Helicase at Lagging-Strand Protein Barriers Support the Steric Exclusion Model

    doi: 10.1016/j.celrep.2019.01.086

    Figure Lengend Snippet: Single-Molecule Detection of CMG Pausing at a Lagging-Strand Methyltransferase Block (A) Schematic representation of experimental approach used in single-molecule DNA unwinding assays. (B) Images of a sample field of view showing accumulation of EGFP-RPA fluorescence signal at different time points from the addition of EGFP-RPA into the chamber. (C) Example unwinding traces of DNA substrates without a protein barrier. Traces exhibit a signal drop upon completion of unwinding due to dissociation of the leading-strand template (depicted in A). (D) Distribution of average fork rates measured in fully unwound substrates without MH (black) and after bypassing MH Lag (blue). Number of molecules are n(-MH) = 199, n(MH Lag after pause) = 20. (E) Sample unwinding traces of DNA substrates modified with MH Lag . Pausing observed at 800 bp is highlighted with gray rectangle. (F) Distribution of pause durations observed in molecules exhibiting a pausing event (n = 109). The solid line is a fit to a single exponential. See also Figure S6 .

    Article Snippet: 5FdC-modified fork templates were mixed with HpaII methyltransferase (M.HpaII) in 1:4 DNA to protein molar ratio in methyltransferase buffer (50 mM Tris-HCl, pH 7.5, 0.5 mM 2-mercaptoethanol (β-ME), 10 mM EDTA, NEB) supplemented with 100 μM S-adenosylmethionine (NEB), and incubated at 37°C for 3 hours.

    Techniques: Blocking Assay, Recombinase Polymerase Amplification, Fluorescence, Modification