taq dna polymerase supertaq  (New England Biolabs)


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    New England Biolabs taq dna polymerase supertaq
    <t>DNA</t> modification and bypass during bisulfite treatment. ( A ) Scheme of the chemical reaction of cytidine: Treatment with bisulfite generates the non-aromatic, non-planar 5,6-dihydrouridine-6-sulfonate (dhU6S), which decomposes to uracil upon treatment with base (and heat). ( B ) Primer extension activity of different polymerases <t>(Taq,</t> 5D4, 3A10, E10, TgoT) on template T1 either unmodified (C), bisulfite-treated and desulfonated (Reagent 1, 80°C, 20 min) (converting dC to dU) (D) or bisulfite-treated (Reagent 1) but not desulphonated (converting dC to dhU6S) (S). Polymerases 5D4 and 3A10 are able to generate full-length (+20) products even from the non-desulphonated template (S). ( C ) Time-course comparison of primer extension activity of Taq and 5D4 on T1 either unmodified (C) or bisulfite-treated with (D) or without desulphonation (S). (P: primer).
    Taq Dna Polymerase Supertaq, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Price from $9.99 to $1999.99
    taq dna polymerase supertaq - by Bioz Stars, 2020-04
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    Related Products / Commonly Used Together

    q5 polymerase

    Images

    1) Product Images from "A polymerase engineered for bisulfite sequencing"

    Article Title: A polymerase engineered for bisulfite sequencing

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkv798

    DNA modification and bypass during bisulfite treatment. ( A ) Scheme of the chemical reaction of cytidine: Treatment with bisulfite generates the non-aromatic, non-planar 5,6-dihydrouridine-6-sulfonate (dhU6S), which decomposes to uracil upon treatment with base (and heat). ( B ) Primer extension activity of different polymerases (Taq, 5D4, 3A10, E10, TgoT) on template T1 either unmodified (C), bisulfite-treated and desulfonated (Reagent 1, 80°C, 20 min) (converting dC to dU) (D) or bisulfite-treated (Reagent 1) but not desulphonated (converting dC to dhU6S) (S). Polymerases 5D4 and 3A10 are able to generate full-length (+20) products even from the non-desulphonated template (S). ( C ) Time-course comparison of primer extension activity of Taq and 5D4 on T1 either unmodified (C) or bisulfite-treated with (D) or without desulphonation (S). (P: primer).
    Figure Legend Snippet: DNA modification and bypass during bisulfite treatment. ( A ) Scheme of the chemical reaction of cytidine: Treatment with bisulfite generates the non-aromatic, non-planar 5,6-dihydrouridine-6-sulfonate (dhU6S), which decomposes to uracil upon treatment with base (and heat). ( B ) Primer extension activity of different polymerases (Taq, 5D4, 3A10, E10, TgoT) on template T1 either unmodified (C), bisulfite-treated and desulfonated (Reagent 1, 80°C, 20 min) (converting dC to dU) (D) or bisulfite-treated (Reagent 1) but not desulphonated (converting dC to dhU6S) (S). Polymerases 5D4 and 3A10 are able to generate full-length (+20) products even from the non-desulphonated template (S). ( C ) Time-course comparison of primer extension activity of Taq and 5D4 on T1 either unmodified (C) or bisulfite-treated with (D) or without desulphonation (S). (P: primer).

    Techniques Used: Modification, Activity Assay

    Amplification of 24 individual human genomic loci. Comparison of PCR performance of Taq (top) panel, with two different Taq/5D4 blends (5/1 (middle panel); 10/1 (bottom panel)) on the amplification of 24 different promotor regions in bisulfite-treated and fully desulphonated human genomic DNA. Both blends are able to amplify a significantly larger number of loci than Taq alone and together enable amplification of 18 out of 24 loci (75%).
    Figure Legend Snippet: Amplification of 24 individual human genomic loci. Comparison of PCR performance of Taq (top) panel, with two different Taq/5D4 blends (5/1 (middle panel); 10/1 (bottom panel)) on the amplification of 24 different promotor regions in bisulfite-treated and fully desulphonated human genomic DNA. Both blends are able to amplify a significantly larger number of loci than Taq alone and together enable amplification of 18 out of 24 loci (75%).

    Techniques Used: Amplification, Polymerase Chain Reaction

    PCR amplification of bisulfite-treated plasmid templates. PCR amplification of bisulfite-treated high GC and low GC content templates ranging from 200–600 bp in size using fully desulphonated templates and three different 5D4/Taq blends (1/10, 1/5, 1/1) with progressively lower Taq content and Taq alone on low dC content plasmid regions (top panel) and high dC content plasmid regions (bottom panel). On templates with low dC content (and hence lower levels of dU and residual dhU6S adducts post bisulfite treatment and desulphonation) either Taq or Taq/5D4 polymerase blends with a high amount of Taq perform best. In contrast on the higher dC content templates only blends containing 5D4 yield amplicons with Taq/5D4 blends (10/1; 5/1) superior to 5D4/Taq 1/1 blend, while Taq alone does not yield any amplification products. Thus only 5D4/Taq blends are able to copy the high GC content templates indicating that the blended enzymes are more efficient at copying templates containing sporadic dUs (and dhU6S adducts) and dU homopolymer stretches. Low molecular weight bands result from primer-dimer formation. (M: E-Gel ® Low Range Quantitative DNA Ladder).
    Figure Legend Snippet: PCR amplification of bisulfite-treated plasmid templates. PCR amplification of bisulfite-treated high GC and low GC content templates ranging from 200–600 bp in size using fully desulphonated templates and three different 5D4/Taq blends (1/10, 1/5, 1/1) with progressively lower Taq content and Taq alone on low dC content plasmid regions (top panel) and high dC content plasmid regions (bottom panel). On templates with low dC content (and hence lower levels of dU and residual dhU6S adducts post bisulfite treatment and desulphonation) either Taq or Taq/5D4 polymerase blends with a high amount of Taq perform best. In contrast on the higher dC content templates only blends containing 5D4 yield amplicons with Taq/5D4 blends (10/1; 5/1) superior to 5D4/Taq 1/1 blend, while Taq alone does not yield any amplification products. Thus only 5D4/Taq blends are able to copy the high GC content templates indicating that the blended enzymes are more efficient at copying templates containing sporadic dUs (and dhU6S adducts) and dU homopolymer stretches. Low molecular weight bands result from primer-dimer formation. (M: E-Gel ® Low Range Quantitative DNA Ladder).

    Techniques Used: Polymerase Chain Reaction, Amplification, Plasmid Preparation, Molecular Weight

    Degree of methylation of individual CpG sites. Promoter regions of four genes ( A — prkcdbp , B — dab2ip , C — ptgs2 , D — ezh2) were amplified with either Taq ot 5D4/Taq blends, using bisulfide-treated genomic DNA from normal cells or LNCapP cells as a template and subjected to deep sequencing. Cyan—methylated CpGs, orange—unmethylated CpGs. Individual CpGs are numbered starting from the 5′ end of the amplicon.
    Figure Legend Snippet: Degree of methylation of individual CpG sites. Promoter regions of four genes ( A — prkcdbp , B — dab2ip , C — ptgs2 , D — ezh2) were amplified with either Taq ot 5D4/Taq blends, using bisulfide-treated genomic DNA from normal cells or LNCapP cells as a template and subjected to deep sequencing. Cyan—methylated CpGs, orange—unmethylated CpGs. Individual CpGs are numbered starting from the 5′ end of the amplicon.

    Techniques Used: Methylation, Amplification, Sequencing

    Related Articles

    Clone Assay:

    Article Title: DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature
    Article Snippet: S.A. or Taq DNA polymerase with standard Taq buffer, New England Biolabs, Inc.), and 1 μ L as a template for 23 and 29 cycles using Eppendorf 5330 thermocycler. .. It was cloned into the pBlue vector and next into expression pT7RSNHU vector at the Nde I and BamH I sites.

    Article Title: Examining Sources of Error in PCR by Single-Molecule Sequencing
    Article Snippet: Q5 High Fidelity DNA Polymerase (#M0491), Phusion High Fidelity DNA Polymerase (#M0530), Deep Vent DNA Polymerase (#M0258), and Taq DNA polymerase (#M0273) are supplied by New England Biolabs. .. Other polymerases were purchased from: Cloned Pfu DNA Polymerase (Agilent Technologies, #600153), Kapa HiFi HotStart ReadyMix (Kapa Biosystems, #KK2602), KOD DNA Polymerase (Novagen, EMD Millipore # 71085–3), PrimeSTAR GXL DNA Polymerase (Clontech, Takara #R050A).

    Amplification:

    Article Title: DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature
    Article Snippet: S.A. or Taq DNA polymerase with standard Taq buffer, New England Biolabs, Inc.), and 1 μ L as a template for 23 and 29 cycles using Eppendorf 5330 thermocycler. .. The amplified 302 bp long DNA fragment was isolated by 1% agarose gel electrophoresis ( ).

    Article Title: One step construction of PCR mutagenized libraries for genetic analysis by recombination cloning
    Article Snippet: Approximately 5 ng of template DNA was added to a reaction containing 5 μl 10× Buffer B (10 mM Tris-HCl pH 9.0, 50 mM KCl final concentration), 5 μl 10 pmol/μl JB.45 (final 1 pmol/μl), 5 μl 10 pmol/μl JB.57 (final 1 pmol/μl), 3.5 μl 25 mM MgCl2 (final 1.75 mM), 0.25 μl of 25 mM MnCl2 (final 0.125 mM), 4.3 μl of 10 mg/ml BSA, 1 μl of 10 mM dNTPs, 1 μl 10 mM dTTP, 1 μl 10 mM dCTP (final 200 μM dATP, 200 μM dGTP, 400 μM dTTP and 400 μM dCTP), 1.5 μl of 5 U/μl concentration Taq DNA polymerase (New England Biolabs), adjusted with H2 O to a volume of 50 μl. .. Reactions were amplified using MJ Research PTC-100 thermal cyclers with an initial denaturation step of 2 min 92°C, followed by 35–40 cycles of 10 s 92°C, 1 min 30 s 65°C, 41/2 min at 72°C and a final 15 min extension at 72°C.

    Article Title: Examining Sources of Error in PCR by Single-Molecule Sequencing
    Article Snippet: PCR Each amplification reaction was set up according to the manufacturer’s suggested protocols. .. Q5 High Fidelity DNA Polymerase (#M0491), Phusion High Fidelity DNA Polymerase (#M0530), Deep Vent DNA Polymerase (#M0258), and Taq DNA polymerase (#M0273) are supplied by New England Biolabs.

    Article Title: Restriction enzyme-free mutagenesis via the light regulation of DNA polymerization
    Article Snippet: In order to visualize truncated products we amplified a 45-mer with either Taq DNA polymerase or Phusion DNA polymerase ( ). .. Each PCR was conducted with one of the forward primers ( WT , P1 , P2 or P3 ), a radioactively labelled reverse primer (Integrated DNA Technologies; 50 pmol), DNA template (1 ng), dNTPs and either Taq DNA polymerase (New England Biolabs, five units) or Phusion DNA Polymerase (New England Biolabs, two units) for 30 cycles.

    Positive Control:

    Article Title: Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs
    Article Snippet: .. Aliquots containing 2.5 U of Taq DNA polymerase (New England Biolabs) were used as a positive control. .. Each of the Dpo4 enzymes was added to a concentration of 200 nM, except the Ssh Dpo4-like enzyme, which was added to a concentration of 400 nM.

    Incubation:

    Article Title: RNase H1 directs origin-specific initiation of DNA replication in human mitochondria
    Article Snippet: Primer extension Isolated DNA (1.8 μg) was incubated for 1 hour at 37°C with or without RNase H2 (NEB). .. Primer extension was performed with 2 U Taq DNA polymerase (NEB) in 1X ThermoPol buffer, 200 μM dNTPs and 1.5 pmol labeled primer.

    Article Title: High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿ †
    Article Snippet: .. Two primers specific to vector-host DNA junctions, LgC (0.1 μM) and RgB (0.1 μM), were bound and linearly extended in the 500-μl reaction solution containing 2.5 to 10 μg of genomic DNA, 1× ThermoPol buffer (New England Biolabs), 0.2 mM deoxynucleoside triphosphates (dNTPs), and 25 units of Taq DNA polymerase (New England Biolabs) under the following conditions: 94°C for 3 min, followed by incubation at 55°C for 5 min and at 72°C for 5 min. To remove single-stranded DNA, the reaction mixture was mixed with 10 units of T7 endonuclease I, 60 units of RecJf , 60 units of exonuclease I, and 1× buffer 4 (New England Biolabs) and incubated at 37°C for 1 h. DNA was purified by phenol and chloroform extractions. .. Double-stranded vector-host junction DNA was digested with Taqα I [(T/C)GA].

    Activity Assay:

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA
    Article Snippet: Enzyme mix PKT was comprised of approximately 1,200 units/ml T4 DNA polymerase, 2,000 units/ml T4 PNK and 2,000 units/ml Taq DNA polymerase (NEB) while PK contained T4 DNA polymerase and T4 PNK only. .. Assays for 3′ A-tailing activity were carried out at 37 °C or 65 °C using annealed oligonucleotides in a final concentration of 0.5 µM and 2 units of Taq DNA pol, Klenow Fragment (3′-5′ exo− ) or Hemo KlenTaq (NEB) in 10 µl reaction in the presence of 1x NEBNext End Repair Buffer (NEB) or a 3′ A tailing buffer.

    Expressing:

    Article Title: DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature
    Article Snippet: S.A. or Taq DNA polymerase with standard Taq buffer, New England Biolabs, Inc.), and 1 μ L as a template for 23 and 29 cycles using Eppendorf 5330 thermocycler. .. It was cloned into the pBlue vector and next into expression pT7RSNHU vector at the Nde I and BamH I sites.

    Modification:

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA
    Article Snippet: Capillary Gel Electrophoresis Analysis Enzyme modification of the DNA substrates was monitored using fluorescence capillary gel electrophoresis (CE) as described previously . .. Enzyme mix PKT was comprised of approximately 1,200 units/ml T4 DNA polymerase, 2,000 units/ml T4 PNK and 2,000 units/ml Taq DNA polymerase (NEB) while PK contained T4 DNA polymerase and T4 PNK only.

    Article Title: High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿ †
    Article Snippet: We modified the inverse-PCR ( ) to amplify both the left and the right vector-cellular DNA junctions simultaneously. .. Two primers specific to vector-host DNA junctions, LgC (0.1 μM) and RgB (0.1 μM), were bound and linearly extended in the 500-μl reaction solution containing 2.5 to 10 μg of genomic DNA, 1× ThermoPol buffer (New England Biolabs), 0.2 mM deoxynucleoside triphosphates (dNTPs), and 25 units of Taq DNA polymerase (New England Biolabs) under the following conditions: 94°C for 3 min, followed by incubation at 55°C for 5 min and at 72°C for 5 min. To remove single-stranded DNA, the reaction mixture was mixed with 10 units of T7 endonuclease I, 60 units of RecJf , 60 units of exonuclease I, and 1× buffer 4 (New England Biolabs) and incubated at 37°C for 1 h. DNA was purified by phenol and chloroform extractions.

    Countercurrent Chromatography:

    Article Title: RNase H1 directs origin-specific initiation of DNA replication in human mitochondria
    Article Snippet: Primer extension was performed with 2 U Taq DNA polymerase (NEB) in 1X ThermoPol buffer, 200 μM dNTPs and 1.5 pmol labeled primer. .. The primers were 5´-end labeled with PNK (NEB) and γ-[32 P]ATP and were corresponding to L-strand positions 8-29 (GGT CTA TCA CCC TAT TAA CCA C) and 16,331-16,351 (CAC ACA TCA ACT GCA ACT CCA).

    Inverse PCR:

    Article Title: High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿ †
    Article Snippet: We modified the inverse-PCR ( ) to amplify both the left and the right vector-cellular DNA junctions simultaneously. .. Two primers specific to vector-host DNA junctions, LgC (0.1 μM) and RgB (0.1 μM), were bound and linearly extended in the 500-μl reaction solution containing 2.5 to 10 μg of genomic DNA, 1× ThermoPol buffer (New England Biolabs), 0.2 mM deoxynucleoside triphosphates (dNTPs), and 25 units of Taq DNA polymerase (New England Biolabs) under the following conditions: 94°C for 3 min, followed by incubation at 55°C for 5 min and at 72°C for 5 min. To remove single-stranded DNA, the reaction mixture was mixed with 10 units of T7 endonuclease I, 60 units of RecJf , 60 units of exonuclease I, and 1× buffer 4 (New England Biolabs) and incubated at 37°C for 1 h. DNA was purified by phenol and chloroform extractions.

    Ligation:

    Article Title: DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature
    Article Snippet: Then, 20 pmol of each phosphorylated (Ubp4′1, Ubp4′3, Ubp4′5, Ubp4′7, Ubp4′9, and Ubp4′11) and unphosphorylated primer (Ubp4′2, Ubp4′4, Ubp4′6, Ubp4′8, and Ubp4′10) was placed in a tube with ligation buffer in a volume of 50 μ L and heated to a temperature of 94°C. .. S.A. or Taq DNA polymerase with standard Taq buffer, New England Biolabs, Inc.), and 1 μ L as a template for 23 and 29 cycles using Eppendorf 5330 thermocycler.

    Article Title: High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿ †
    Article Snippet: Two primers specific to vector-host DNA junctions, LgC (0.1 μM) and RgB (0.1 μM), were bound and linearly extended in the 500-μl reaction solution containing 2.5 to 10 μg of genomic DNA, 1× ThermoPol buffer (New England Biolabs), 0.2 mM deoxynucleoside triphosphates (dNTPs), and 25 units of Taq DNA polymerase (New England Biolabs) under the following conditions: 94°C for 3 min, followed by incubation at 55°C for 5 min and at 72°C for 5 min. To remove single-stranded DNA, the reaction mixture was mixed with 10 units of T7 endonuclease I, 60 units of RecJf , 60 units of exonuclease I, and 1× buffer 4 (New England Biolabs) and incubated at 37°C for 1 h. DNA was purified by phenol and chloroform extractions. .. Digested DNA was purified and ligated under conditions favoring intramolecular ligation.

    other:

    Article Title: Restriction enzyme-free mutagenesis via the light regulation of DNA polymerization
    Article Snippet: These results demonstrate that both Taq DNA polymerase and Phusion DNA polymerase are stopped by a single-caged thymidine.

    Polymerase Chain Reaction:

    Article Title: DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature
    Article Snippet: The PCR was performed in a 50μ L reaction volume with a buffer containing 50 mM KCl, 2 mM MgCl2, 0.02 mM of each dNTP, 75 mM Tris-HCl (pH 8.9), 20 mM (NH4)2SO4, 25 pM of each primer: Ubp4′Rev, Ubp4′For (with additional sequence for restriction enzymes: Nde I, EcoR I, and BamH I), the enzyme Biotools DNA polymerase (Biotools B & M Labs. .. S.A. or Taq DNA polymerase with standard Taq buffer, New England Biolabs, Inc.), and 1 μ L as a template for 23 and 29 cycles using Eppendorf 5330 thermocycler.

    Article Title: One step construction of PCR mutagenized libraries for genetic analysis by recombination cloning
    Article Snippet: Paragraph title: Mutagenic PCR ... Approximately 5 ng of template DNA was added to a reaction containing 5 μl 10× Buffer B (10 mM Tris-HCl pH 9.0, 50 mM KCl final concentration), 5 μl 10 pmol/μl JB.45 (final 1 pmol/μl), 5 μl 10 pmol/μl JB.57 (final 1 pmol/μl), 3.5 μl 25 mM MgCl2 (final 1.75 mM), 0.25 μl of 25 mM MnCl2 (final 0.125 mM), 4.3 μl of 10 mg/ml BSA, 1 μl of 10 mM dNTPs, 1 μl 10 mM dTTP, 1 μl 10 mM dCTP (final 200 μM dATP, 200 μM dGTP, 400 μM dTTP and 400 μM dCTP), 1.5 μl of 5 U/μl concentration Taq DNA polymerase (New England Biolabs), adjusted with H2 O to a volume of 50 μl.

    Article Title: Examining Sources of Error in PCR by Single-Molecule Sequencing
    Article Snippet: Paragraph title: PCR ... Q5 High Fidelity DNA Polymerase (#M0491), Phusion High Fidelity DNA Polymerase (#M0530), Deep Vent DNA Polymerase (#M0258), and Taq DNA polymerase (#M0273) are supplied by New England Biolabs.

    Article Title: Restriction enzyme-free mutagenesis via the light regulation of DNA polymerization
    Article Snippet: .. Each PCR was conducted with one of the forward primers ( WT , P1 , P2 or P3 ), a radioactively labelled reverse primer (Integrated DNA Technologies; 50 pmol), DNA template (1 ng), dNTPs and either Taq DNA polymerase (New England Biolabs, five units) or Phusion DNA Polymerase (New England Biolabs, two units) for 30 cycles. .. The PCR was then run on a polyacrylamide gel to identify PCR termination by the caged nucleotide.

    Nucleic Acid Electrophoresis:

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA
    Article Snippet: Paragraph title: Capillary Gel Electrophoresis Analysis ... Enzyme mix PKT was comprised of approximately 1,200 units/ml T4 DNA polymerase, 2,000 units/ml T4 PNK and 2,000 units/ml Taq DNA polymerase (NEB) while PK contained T4 DNA polymerase and T4 PNK only.

    Fluorescence:

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA
    Article Snippet: Capillary Gel Electrophoresis Analysis Enzyme modification of the DNA substrates was monitored using fluorescence capillary gel electrophoresis (CE) as described previously . .. Enzyme mix PKT was comprised of approximately 1,200 units/ml T4 DNA polymerase, 2,000 units/ml T4 PNK and 2,000 units/ml Taq DNA polymerase (NEB) while PK contained T4 DNA polymerase and T4 PNK only.

    Isolation:

    Article Title: RNase H1 directs origin-specific initiation of DNA replication in human mitochondria
    Article Snippet: Primer extension Isolated DNA (1.8 μg) was incubated for 1 hour at 37°C with or without RNase H2 (NEB). .. Primer extension was performed with 2 U Taq DNA polymerase (NEB) in 1X ThermoPol buffer, 200 μM dNTPs and 1.5 pmol labeled primer.

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA
    Article Snippet: .. Comparison of the 5′ nuclease activities of taq DNA polymerase and its isolated nuclease domain. ..

    Article Title: DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature
    Article Snippet: S.A. or Taq DNA polymerase with standard Taq buffer, New England Biolabs, Inc.), and 1 μ L as a template for 23 and 29 cycles using Eppendorf 5330 thermocycler. .. The amplified 302 bp long DNA fragment was isolated by 1% agarose gel electrophoresis ( ).

    Labeling:

    Article Title: RNase H1 directs origin-specific initiation of DNA replication in human mitochondria
    Article Snippet: .. Primer extension was performed with 2 U Taq DNA polymerase (NEB) in 1X ThermoPol buffer, 200 μM dNTPs and 1.5 pmol labeled primer. .. The primers were 5´-end labeled with PNK (NEB) and γ-[32 P]ATP and were corresponding to L-strand positions 8-29 (GGT CTA TCA CCC TAT TAA CCA C) and 16,331-16,351 (CAC ACA TCA ACT GCA ACT CCA).

    Article Title: CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis
    Article Snippet: .. The two color genome mapping with Cas9n fluorescent nick-labeling and sequence-motif labeling After nicking with Cas9n D10A as previously described in the Cas9n fluorescent nick-labeling section, the sample was digested with RNAseA (190 ng/μL, QIAGEN) at 37°C for 20 min. After digestion, the sample was labeled with ATTO 532-dATP, dTGC (100 nM) and 2.5 units of DNA Taq Polymerase (NEB) in the presence of 1X Thermopol Buffer (NEB) at 72°C for 1 h. The sample was treated with 1 unit of SAP (USB Products) and RNAseA (100 ng/μL) at 37°C for 20 min and then 65°C for 15 min. ..

    Purification:

    Article Title: High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿ †
    Article Snippet: .. Two primers specific to vector-host DNA junctions, LgC (0.1 μM) and RgB (0.1 μM), were bound and linearly extended in the 500-μl reaction solution containing 2.5 to 10 μg of genomic DNA, 1× ThermoPol buffer (New England Biolabs), 0.2 mM deoxynucleoside triphosphates (dNTPs), and 25 units of Taq DNA polymerase (New England Biolabs) under the following conditions: 94°C for 3 min, followed by incubation at 55°C for 5 min and at 72°C for 5 min. To remove single-stranded DNA, the reaction mixture was mixed with 10 units of T7 endonuclease I, 60 units of RecJf , 60 units of exonuclease I, and 1× buffer 4 (New England Biolabs) and incubated at 37°C for 1 h. DNA was purified by phenol and chloroform extractions. .. Double-stranded vector-host junction DNA was digested with Taqα I [(T/C)GA].

    Sequencing:

    Article Title: CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis
    Article Snippet: .. The two color genome mapping with Cas9n fluorescent nick-labeling and sequence-motif labeling After nicking with Cas9n D10A as previously described in the Cas9n fluorescent nick-labeling section, the sample was digested with RNAseA (190 ng/μL, QIAGEN) at 37°C for 20 min. After digestion, the sample was labeled with ATTO 532-dATP, dTGC (100 nM) and 2.5 units of DNA Taq Polymerase (NEB) in the presence of 1X Thermopol Buffer (NEB) at 72°C for 1 h. The sample was treated with 1 unit of SAP (USB Products) and RNAseA (100 ng/μL) at 37°C for 20 min and then 65°C for 15 min. ..

    Article Title: DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature
    Article Snippet: The PCR was performed in a 50μ L reaction volume with a buffer containing 50 mM KCl, 2 mM MgCl2, 0.02 mM of each dNTP, 75 mM Tris-HCl (pH 8.9), 20 mM (NH4)2SO4, 25 pM of each primer: Ubp4′Rev, Ubp4′For (with additional sequence for restriction enzymes: Nde I, EcoR I, and BamH I), the enzyme Biotools DNA polymerase (Biotools B & M Labs. .. S.A. or Taq DNA polymerase with standard Taq buffer, New England Biolabs, Inc.), and 1 μ L as a template for 23 and 29 cycles using Eppendorf 5330 thermocycler.

    Activated Clotting Time Assay:

    Article Title: RNase H1 directs origin-specific initiation of DNA replication in human mitochondria
    Article Snippet: Primer extension was performed with 2 U Taq DNA polymerase (NEB) in 1X ThermoPol buffer, 200 μM dNTPs and 1.5 pmol labeled primer. .. The primers were 5´-end labeled with PNK (NEB) and γ-[32 P]ATP and were corresponding to L-strand positions 8-29 (GGT CTA TCA CCC TAT TAA CCA C) and 16,331-16,351 (CAC ACA TCA ACT GCA ACT CCA).

    Plasmid Preparation:

    Article Title: DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature
    Article Snippet: S.A. or Taq DNA polymerase with standard Taq buffer, New England Biolabs, Inc.), and 1 μ L as a template for 23 and 29 cycles using Eppendorf 5330 thermocycler. .. It was cloned into the pBlue vector and next into expression pT7RSNHU vector at the Nde I and BamH I sites.

    Article Title: Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs
    Article Snippet: PCRs on undamaged DNA For the undamaged plasmid DNA template, 50 µl PCRs were set up containing standard ThermoPol reaction buffer [20 mM Tris–HCl, pH 8.8, 10 mM KCl, 10 mM (NH4 )2 SO4 , 2 mM MgSO4 , 0.1% Triton X-100] (New England Biolabs), 10 ng of circular pJM548 (Ste dpo4 -like in pGEM-T), 200 µM of each ultrapure dNTP and 1 µM of each primer; Ste_FNde5 and Ste_RBam1089 whose sequences are provided above. .. Aliquots containing 2.5 U of Taq DNA polymerase (New England Biolabs) were used as a positive control.

    Article Title: Examining Sources of Error in PCR by Single-Molecule Sequencing
    Article Snippet: Q5 High Fidelity DNA Polymerase (#M0491), Phusion High Fidelity DNA Polymerase (#M0530), Deep Vent DNA Polymerase (#M0258), and Taq DNA polymerase (#M0273) are supplied by New England Biolabs. .. Reaction conditions ranged from: 1X reaction buffer (provided with the enzyme), 200–300 μM each dNTP, 0.2–1 μM forward and reverse primers, 100 pg/μl plasmid template (linearized with a restriction enzyme and treated with PreCR) and polymerase.

    Article Title: High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿High-Throughput, Sensitive Quantification of Repopulating Hematopoietic Stem Cell Clones ▿ †
    Article Snippet: .. Two primers specific to vector-host DNA junctions, LgC (0.1 μM) and RgB (0.1 μM), were bound and linearly extended in the 500-μl reaction solution containing 2.5 to 10 μg of genomic DNA, 1× ThermoPol buffer (New England Biolabs), 0.2 mM deoxynucleoside triphosphates (dNTPs), and 25 units of Taq DNA polymerase (New England Biolabs) under the following conditions: 94°C for 3 min, followed by incubation at 55°C for 5 min and at 72°C for 5 min. To remove single-stranded DNA, the reaction mixture was mixed with 10 units of T7 endonuclease I, 60 units of RecJf , 60 units of exonuclease I, and 1× buffer 4 (New England Biolabs) and incubated at 37°C for 1 h. DNA was purified by phenol and chloroform extractions. .. Double-stranded vector-host junction DNA was digested with Taqα I [(T/C)GA].

    Agarose Gel Electrophoresis:

    Article Title: DNASynth: A Computer Program for Assembly of Artificial Gene Parts in Decreasing Temperature
    Article Snippet: S.A. or Taq DNA polymerase with standard Taq buffer, New England Biolabs, Inc.), and 1 μ L as a template for 23 and 29 cycles using Eppendorf 5330 thermocycler. .. The amplified 302 bp long DNA fragment was isolated by 1% agarose gel electrophoresis ( ).

    Article Title: Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs
    Article Snippet: Aliquots containing 2.5 U of Taq DNA polymerase (New England Biolabs) were used as a positive control. .. Reactions were heated to 85°C for 3 min and then treated with 35 cycles of 85°C for 30 s, 56°C for 1 min and 60°C for 4 min. Products were separated on a 0.9% agarose gel stained with ethidium bromide.

    Concentration Assay:

    Article Title: Solid-phase enzyme catalysis of DNA end repair and 3′ A-tailing reduces GC-bias in next-generation sequencing of human genomic DNA
    Article Snippet: Enzyme mix PKT was comprised of approximately 1,200 units/ml T4 DNA polymerase, 2,000 units/ml T4 PNK and 2,000 units/ml Taq DNA polymerase (NEB) while PK contained T4 DNA polymerase and T4 PNK only. .. Assays for 3′ A-tailing activity were carried out at 37 °C or 65 °C using annealed oligonucleotides in a final concentration of 0.5 µM and 2 units of Taq DNA pol, Klenow Fragment (3′-5′ exo− ) or Hemo KlenTaq (NEB) in 10 µl reaction in the presence of 1x NEBNext End Repair Buffer (NEB) or a 3′ A tailing buffer.

    Article Title: Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs
    Article Snippet: Aliquots containing 2.5 U of Taq DNA polymerase (New England Biolabs) were used as a positive control. .. Each of the Dpo4 enzymes was added to a concentration of 200 nM, except the Ssh Dpo4-like enzyme, which was added to a concentration of 400 nM.

    Article Title: One step construction of PCR mutagenized libraries for genetic analysis by recombination cloning
    Article Snippet: .. Approximately 5 ng of template DNA was added to a reaction containing 5 μl 10× Buffer B (10 mM Tris-HCl pH 9.0, 50 mM KCl final concentration), 5 μl 10 pmol/μl JB.45 (final 1 pmol/μl), 5 μl 10 pmol/μl JB.57 (final 1 pmol/μl), 3.5 μl 25 mM MgCl2 (final 1.75 mM), 0.25 μl of 25 mM MnCl2 (final 0.125 mM), 4.3 μl of 10 mg/ml BSA, 1 μl of 10 mM dNTPs, 1 μl 10 mM dTTP, 1 μl 10 mM dCTP (final 200 μM dATP, 200 μM dGTP, 400 μM dTTP and 400 μM dCTP), 1.5 μl of 5 U/μl concentration Taq DNA polymerase (New England Biolabs), adjusted with H2 O to a volume of 50 μl. ..

    Staining:

    Article Title: Novel thermostable Y-family polymerases: applications for the PCR amplification of damaged or ancient DNAs
    Article Snippet: Aliquots containing 2.5 U of Taq DNA polymerase (New England Biolabs) were used as a positive control. .. Reactions were heated to 85°C for 3 min and then treated with 35 cycles of 85°C for 30 s, 56°C for 1 min and 60°C for 4 min. Products were separated on a 0.9% agarose gel stained with ethidium bromide.

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    New England Biolabs taq dna polymerase supertaq
    <t>DNA</t> modification and bypass during bisulfite treatment. ( A ) Scheme of the chemical reaction of cytidine: Treatment with bisulfite generates the non-aromatic, non-planar 5,6-dihydrouridine-6-sulfonate (dhU6S), which decomposes to uracil upon treatment with base (and heat). ( B ) Primer extension activity of different polymerases <t>(Taq,</t> 5D4, 3A10, E10, TgoT) on template T1 either unmodified (C), bisulfite-treated and desulfonated (Reagent 1, 80°C, 20 min) (converting dC to dU) (D) or bisulfite-treated (Reagent 1) but not desulphonated (converting dC to dhU6S) (S). Polymerases 5D4 and 3A10 are able to generate full-length (+20) products even from the non-desulphonated template (S). ( C ) Time-course comparison of primer extension activity of Taq and 5D4 on T1 either unmodified (C) or bisulfite-treated with (D) or without desulphonation (S). (P: primer).
    Taq Dna Polymerase Supertaq, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    taq dna polymerase supertaq - by Bioz Stars, 2020-04
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    DNA modification and bypass during bisulfite treatment. ( A ) Scheme of the chemical reaction of cytidine: Treatment with bisulfite generates the non-aromatic, non-planar 5,6-dihydrouridine-6-sulfonate (dhU6S), which decomposes to uracil upon treatment with base (and heat). ( B ) Primer extension activity of different polymerases (Taq, 5D4, 3A10, E10, TgoT) on template T1 either unmodified (C), bisulfite-treated and desulfonated (Reagent 1, 80°C, 20 min) (converting dC to dU) (D) or bisulfite-treated (Reagent 1) but not desulphonated (converting dC to dhU6S) (S). Polymerases 5D4 and 3A10 are able to generate full-length (+20) products even from the non-desulphonated template (S). ( C ) Time-course comparison of primer extension activity of Taq and 5D4 on T1 either unmodified (C) or bisulfite-treated with (D) or without desulphonation (S). (P: primer).

    Journal: Nucleic Acids Research

    Article Title: A polymerase engineered for bisulfite sequencing

    doi: 10.1093/nar/gkv798

    Figure Lengend Snippet: DNA modification and bypass during bisulfite treatment. ( A ) Scheme of the chemical reaction of cytidine: Treatment with bisulfite generates the non-aromatic, non-planar 5,6-dihydrouridine-6-sulfonate (dhU6S), which decomposes to uracil upon treatment with base (and heat). ( B ) Primer extension activity of different polymerases (Taq, 5D4, 3A10, E10, TgoT) on template T1 either unmodified (C), bisulfite-treated and desulfonated (Reagent 1, 80°C, 20 min) (converting dC to dU) (D) or bisulfite-treated (Reagent 1) but not desulphonated (converting dC to dhU6S) (S). Polymerases 5D4 and 3A10 are able to generate full-length (+20) products even from the non-desulphonated template (S). ( C ) Time-course comparison of primer extension activity of Taq and 5D4 on T1 either unmodified (C) or bisulfite-treated with (D) or without desulphonation (S). (P: primer).

    Article Snippet: Taq DNA polymerase (SuperTaq) was obtained from HT Biotechnology (Cambridge) and Q5 polymerase from New England Biolabs.

    Techniques: Modification, Activity Assay

    Amplification of 24 individual human genomic loci. Comparison of PCR performance of Taq (top) panel, with two different Taq/5D4 blends (5/1 (middle panel); 10/1 (bottom panel)) on the amplification of 24 different promotor regions in bisulfite-treated and fully desulphonated human genomic DNA. Both blends are able to amplify a significantly larger number of loci than Taq alone and together enable amplification of 18 out of 24 loci (75%).

    Journal: Nucleic Acids Research

    Article Title: A polymerase engineered for bisulfite sequencing

    doi: 10.1093/nar/gkv798

    Figure Lengend Snippet: Amplification of 24 individual human genomic loci. Comparison of PCR performance of Taq (top) panel, with two different Taq/5D4 blends (5/1 (middle panel); 10/1 (bottom panel)) on the amplification of 24 different promotor regions in bisulfite-treated and fully desulphonated human genomic DNA. Both blends are able to amplify a significantly larger number of loci than Taq alone and together enable amplification of 18 out of 24 loci (75%).

    Article Snippet: Taq DNA polymerase (SuperTaq) was obtained from HT Biotechnology (Cambridge) and Q5 polymerase from New England Biolabs.

    Techniques: Amplification, Polymerase Chain Reaction

    PCR amplification of bisulfite-treated plasmid templates. PCR amplification of bisulfite-treated high GC and low GC content templates ranging from 200–600 bp in size using fully desulphonated templates and three different 5D4/Taq blends (1/10, 1/5, 1/1) with progressively lower Taq content and Taq alone on low dC content plasmid regions (top panel) and high dC content plasmid regions (bottom panel). On templates with low dC content (and hence lower levels of dU and residual dhU6S adducts post bisulfite treatment and desulphonation) either Taq or Taq/5D4 polymerase blends with a high amount of Taq perform best. In contrast on the higher dC content templates only blends containing 5D4 yield amplicons with Taq/5D4 blends (10/1; 5/1) superior to 5D4/Taq 1/1 blend, while Taq alone does not yield any amplification products. Thus only 5D4/Taq blends are able to copy the high GC content templates indicating that the blended enzymes are more efficient at copying templates containing sporadic dUs (and dhU6S adducts) and dU homopolymer stretches. Low molecular weight bands result from primer-dimer formation. (M: E-Gel ® Low Range Quantitative DNA Ladder).

    Journal: Nucleic Acids Research

    Article Title: A polymerase engineered for bisulfite sequencing

    doi: 10.1093/nar/gkv798

    Figure Lengend Snippet: PCR amplification of bisulfite-treated plasmid templates. PCR amplification of bisulfite-treated high GC and low GC content templates ranging from 200–600 bp in size using fully desulphonated templates and three different 5D4/Taq blends (1/10, 1/5, 1/1) with progressively lower Taq content and Taq alone on low dC content plasmid regions (top panel) and high dC content plasmid regions (bottom panel). On templates with low dC content (and hence lower levels of dU and residual dhU6S adducts post bisulfite treatment and desulphonation) either Taq or Taq/5D4 polymerase blends with a high amount of Taq perform best. In contrast on the higher dC content templates only blends containing 5D4 yield amplicons with Taq/5D4 blends (10/1; 5/1) superior to 5D4/Taq 1/1 blend, while Taq alone does not yield any amplification products. Thus only 5D4/Taq blends are able to copy the high GC content templates indicating that the blended enzymes are more efficient at copying templates containing sporadic dUs (and dhU6S adducts) and dU homopolymer stretches. Low molecular weight bands result from primer-dimer formation. (M: E-Gel ® Low Range Quantitative DNA Ladder).

    Article Snippet: Taq DNA polymerase (SuperTaq) was obtained from HT Biotechnology (Cambridge) and Q5 polymerase from New England Biolabs.

    Techniques: Polymerase Chain Reaction, Amplification, Plasmid Preparation, Molecular Weight

    Degree of methylation of individual CpG sites. Promoter regions of four genes ( A — prkcdbp , B — dab2ip , C — ptgs2 , D — ezh2) were amplified with either Taq ot 5D4/Taq blends, using bisulfide-treated genomic DNA from normal cells or LNCapP cells as a template and subjected to deep sequencing. Cyan—methylated CpGs, orange—unmethylated CpGs. Individual CpGs are numbered starting from the 5′ end of the amplicon.

    Journal: Nucleic Acids Research

    Article Title: A polymerase engineered for bisulfite sequencing

    doi: 10.1093/nar/gkv798

    Figure Lengend Snippet: Degree of methylation of individual CpG sites. Promoter regions of four genes ( A — prkcdbp , B — dab2ip , C — ptgs2 , D — ezh2) were amplified with either Taq ot 5D4/Taq blends, using bisulfide-treated genomic DNA from normal cells or LNCapP cells as a template and subjected to deep sequencing. Cyan—methylated CpGs, orange—unmethylated CpGs. Individual CpGs are numbered starting from the 5′ end of the amplicon.

    Article Snippet: Taq DNA polymerase (SuperTaq) was obtained from HT Biotechnology (Cambridge) and Q5 polymerase from New England Biolabs.

    Techniques: Methylation, Amplification, Sequencing