taq polymerase Thermo Fisher Search Results


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  • 95
    New England Biolabs taq
    Taq, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 1068 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 95 stars, based on 1068 article reviews
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    taq - by Bioz Stars, 2020-02
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    95
    Millipore taq polymerase
    Taq Polymerase, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 2360 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher taq dna polymerase
    Differential peak morphologies of androgen receptor alleles resulting from <t>DNA</t> dilution and reagent use. Lynx positive control DNA sample amplified with Invitrogen <t>Taq</t> DNA Polymerase and diluted to 1:10 ( a ), 1:20 ( b ), and 1:50 ( c ) ratios with deionized water. Lynx positive control DNA sample amplified with Invitrogen Platinum Taq DNA Polymerase (no dilution necessary) ( d )
    Taq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 36264 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Fisher Scientific taq polymerase
    Differential peak morphologies of androgen receptor alleles resulting from <t>DNA</t> dilution and reagent use. Lynx positive control DNA sample amplified with Invitrogen <t>Taq</t> DNA Polymerase and diluted to 1:10 ( a ), 1:20 ( b ), and 1:50 ( c ) ratios with deionized water. Lynx positive control DNA sample amplified with Invitrogen Platinum Taq DNA Polymerase (no dilution necessary) ( d )
    Taq Polymerase, supplied by Fisher Scientific, used in various techniques. Bioz Stars score: 96/100, based on 345 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 96 stars, based on 345 article reviews
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    94
    Fisher Bioreagents taq polymerase
    Differential peak morphologies of androgen receptor alleles resulting from <t>DNA</t> dilution and reagent use. Lynx positive control DNA sample amplified with Invitrogen <t>Taq</t> DNA Polymerase and diluted to 1:10 ( a ), 1:20 ( b ), and 1:50 ( c ) ratios with deionized water. Lynx positive control DNA sample amplified with Invitrogen Platinum Taq DNA Polymerase (no dilution necessary) ( d )
    Taq Polymerase, supplied by Fisher Bioreagents, used in various techniques. Bioz Stars score: 94/100, based on 18 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    5 PRIME taq polymerase
    Differential peak morphologies of androgen receptor alleles resulting from <t>DNA</t> dilution and reagent use. Lynx positive control DNA sample amplified with Invitrogen <t>Taq</t> DNA Polymerase and diluted to 1:10 ( a ), 1:20 ( b ), and 1:50 ( c ) ratios with deionized water. Lynx positive control DNA sample amplified with Invitrogen Platinum Taq DNA Polymerase (no dilution necessary) ( d )
    Taq Polymerase, supplied by 5 PRIME, used in various techniques. Bioz Stars score: 96/100, based on 284 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher thermoprime taq polymerase
    Differential peak morphologies of androgen receptor alleles resulting from <t>DNA</t> dilution and reagent use. Lynx positive control DNA sample amplified with Invitrogen <t>Taq</t> DNA Polymerase and diluted to 1:10 ( a ), 1:20 ( b ), and 1:50 ( c ) ratios with deionized water. Lynx positive control DNA sample amplified with Invitrogen Platinum Taq DNA Polymerase (no dilution necessary) ( d )
    Thermoprime Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher accuprime taq dna polymerase high fidelity
    'PER' genome-wide base composition bias curves . (a,b) Shown is the GC bias in Illumina reads from a 400-bp fragment library amplified using the standard PCR protocol (Phusion HF, short denaturation) on a fast-ramping thermocycler (red squares), Phusion HF with long denaturation and 2M betaine (black triangles), <t>AccuPrime</t> <t>Taq</t> HiFi with long denaturation and primer extension at 65°C (blue diamonds) or 60°C (purple diamonds). To calculate the observed to expected (unbiased) read coverage, the number of reads aligning to 50-bp windows at a given %GC was divided by the number of 50-bp windows that fall in this %GC category. This value was then normalized relative to the average value from 48% through 52% GC and plotted on a log 10 scale (a) or linear scale (b).
    Accuprime Taq Dna Polymerase High Fidelity, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 1178 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher platinum taq dna polymerase
    Confirmation of spy0129 Deletion Mutant and Adherence Assay Top panel is a schematic representation of the spy0127–0130 cluster. Position of primers for RT-PCR are indicated by arrows. (A) Results of RT-PCR analysis on mRNA from two putative deletion mutants (Δ1 and Δ2) and the parental SF370 strain (P). mRNA was isolated from mid log-phase or stationary phase cells (indicated below panel) and reverse-transcribed with two primer combinations, which are indicated at the top of the lanes as primer set A (0129F–0129R) and primer set B (0129F–0130R). cDNA products were separated on a 1% agarose gel and visualized by ethidium bromide staining. The expected sizes of resulting cDNAs from SF370 using primer set A is 365 bp and using primer set B is 1200 bp. Control reactions (C) containing mid-log phase mRNA and <t>Taq</t> <t>DNA</t> polymerase instead of reverse transcriptase are indicated. Lane 1 contains 1 kb Plus DNA ladder (1 μg; Invitrogen). (B) Results of the pharyngeal cell adherence assay (detailed in Methods), comparing parental strain SF370 to the spy0129–0130 isogenic mutant, SF370Δ spy0129 .2 (abbreviated as Δ spy0129 ). Adherent streptococci are reported as the percentage of total number of streptococci added as inoculum to pharyngeal cell monolayers. Statistical significance (reported as p -value) was determined by Student's t- test.
    Platinum Taq Dna Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 19955 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    90
    Thermo Fisher taq dna polymerase primer extension
    PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of <t>DNA</t> polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with <t>Taq</t> DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.
    Taq Dna Polymerase Primer Extension, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 90/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher phusion taq polymerase
    PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of <t>DNA</t> polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with <t>Taq</t> DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.
    Phusion Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 306 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Thermo Fisher faststart taq polymerase
    PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of <t>DNA</t> polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with <t>Taq</t> DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.
    Faststart Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Thermo Fisher elongase taq polymerase
    PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of <t>DNA</t> polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with <t>Taq</t> DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.
    Elongase Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 89/100, based on 28 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher hifi taq polymerase
    PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of <t>DNA</t> polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with <t>Taq</t> DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.
    Hifi Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 129 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    99
    Thermo Fisher accuprime taq polymerase
    PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of <t>DNA</t> polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with <t>Taq</t> DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.
    Accuprime Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 404 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Thermo Fisher recombiant taq polymerase
    PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of <t>DNA</t> polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with <t>Taq</t> DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.
    Recombiant Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    Fisher Bioreagents taq polymerase buffer
    PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of <t>DNA</t> polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with <t>Taq</t> DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.
    Taq Polymerase Buffer, supplied by Fisher Bioreagents, used in various techniques. Bioz Stars score: 88/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    97
    Roche taq dna polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Taq Dna Polymerase, supplied by Roche, used in various techniques. Bioz Stars score: 97/100, based on 6706 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Thermo Fisher platinium taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Platinium Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 124 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    Thermo Fisher ofplatinum taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Ofplatinum Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 80/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    78
    Thermo Fisher redman taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Redman Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 78/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Thermo Fisher ampli taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Ampli Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 109 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    76
    Thermo Fisher hotstart it taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Hotstart It Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 76/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    83
    Thermo Fisher thermostart taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Thermostart Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 83/100, based on 32 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    95
    Thermo Fisher taq polymerase buffer
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Taq Polymerase Buffer, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 95/100, based on 500 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    87
    Thermo Fisher phire taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Phire Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 87/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    79
    Thermo Fisher 1unit taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    1unit Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 79/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher ampligold taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Ampligold Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 82/100, based on 19 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    82
    Fisher Bioreagents standard taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Standard Taq Polymerase, supplied by Fisher Bioreagents, used in various techniques. Bioz Stars score: 82/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    77
    Thermo Fisher pyrostart taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Pyrostart Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 77/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Thermo Fisher standard taq polymerase
    Dependencies of apparent rate of substrate binding by <t>DNA</t> polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – <t>Taq</t> polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)
    Standard Taq Polymerase, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 96/100, based on 121 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Differential peak morphologies of androgen receptor alleles resulting from DNA dilution and reagent use. Lynx positive control DNA sample amplified with Invitrogen Taq DNA Polymerase and diluted to 1:10 ( a ), 1:20 ( b ), and 1:50 ( c ) ratios with deionized water. Lynx positive control DNA sample amplified with Invitrogen Platinum Taq DNA Polymerase (no dilution necessary) ( d )

    Journal: BMC Genetics

    Article Title: A test of somatic mosaicism in the androgen receptor gene of Canada lynx (Lynx canadensis)

    doi: 10.1186/s12863-015-0284-y

    Figure Lengend Snippet: Differential peak morphologies of androgen receptor alleles resulting from DNA dilution and reagent use. Lynx positive control DNA sample amplified with Invitrogen Taq DNA Polymerase and diluted to 1:10 ( a ), 1:20 ( b ), and 1:50 ( c ) ratios with deionized water. Lynx positive control DNA sample amplified with Invitrogen Platinum Taq DNA Polymerase (no dilution necessary) ( d )

    Article Snippet: Amplification was conducted in a 10ul reaction containing deionized water (Invitrogen), 10X PCR Reaction Buffer (Invitrogen), 50 mM MgCl2 (Invitrogen), 100 mM dNTP solution (Invitrogen), 3 mg/mL BSA, 40uM forward and reverse primers (Integrated DNA Technologies) mentioned above (forward primers labeled with the fluorescent dye HEX), 0.0375U Invitrogen Taq DNA Polymerase, and 5 ng of DNA.

    Techniques: Positive Control, Amplification

    'PER' genome-wide base composition bias curves . (a,b) Shown is the GC bias in Illumina reads from a 400-bp fragment library amplified using the standard PCR protocol (Phusion HF, short denaturation) on a fast-ramping thermocycler (red squares), Phusion HF with long denaturation and 2M betaine (black triangles), AccuPrime Taq HiFi with long denaturation and primer extension at 65°C (blue diamonds) or 60°C (purple diamonds). To calculate the observed to expected (unbiased) read coverage, the number of reads aligning to 50-bp windows at a given %GC was divided by the number of 50-bp windows that fall in this %GC category. This value was then normalized relative to the average value from 48% through 52% GC and plotted on a log 10 scale (a) or linear scale (b).

    Journal: Genome Biology

    Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

    doi: 10.1186/gb-2011-12-2-r18

    Figure Lengend Snippet: 'PER' genome-wide base composition bias curves . (a,b) Shown is the GC bias in Illumina reads from a 400-bp fragment library amplified using the standard PCR protocol (Phusion HF, short denaturation) on a fast-ramping thermocycler (red squares), Phusion HF with long denaturation and 2M betaine (black triangles), AccuPrime Taq HiFi with long denaturation and primer extension at 65°C (blue diamonds) or 60°C (purple diamonds). To calculate the observed to expected (unbiased) read coverage, the number of reads aligning to 50-bp windows at a given %GC was divided by the number of 50-bp windows that fall in this %GC category. This value was then normalized relative to the average value from 48% through 52% GC and plotted on a log 10 scale (a) or linear scale (b).

    Article Snippet: One unit of AccuPrime Taq DNA polymerase High Fidelity (Invitrogen) was used in 50 μl 1× AccuPrime PCR buffer II.

    Techniques: Genome Wide, Amplification, Polymerase Chain Reaction

    Sequencing bias with PCR-amplified and PCR-free libraries . (a,b) Shown is the mean normalized coverage of 50-bp windows in the human genome having the GC-content indicated on the x-axis for a PCR-free (orange dots) and a PCR-amplified (blue diamonds) Illumina sequencing library. Both fragment libraries had approximately 180-bp inserts. The PCR amplification was performed with AccuPrime Taq HiFi (long denat., primer extension at 65°C). The coverage was plotted on a log 10 (a) and a linear scale (b). The data points at extremely high GC, where the reads from the PCR-free library had a mean base quality of less than Q20 (open symbols), were omitted in the middle panel (b). (c) The ratios of the two curves in (a,b), that is, the fold-increase in mean coverage by sequencing a PCR-free library instead of a PCR-amplified library. The shaded histogram is the %GC distribution of 50-bp windows in the human genome. More than 99.9% of all 50-bp windows in the genome contain 8% to 88% GC and received a less than 1.25-fold increase in coverage. Less than 0.01% of all 50-bp windows contain 90% or more GC. The open circles at 96% and 98% GC denote data for which the mean base quality of the reads from the PCR-free library was below Q20.

    Journal: Genome Biology

    Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

    doi: 10.1186/gb-2011-12-2-r18

    Figure Lengend Snippet: Sequencing bias with PCR-amplified and PCR-free libraries . (a,b) Shown is the mean normalized coverage of 50-bp windows in the human genome having the GC-content indicated on the x-axis for a PCR-free (orange dots) and a PCR-amplified (blue diamonds) Illumina sequencing library. Both fragment libraries had approximately 180-bp inserts. The PCR amplification was performed with AccuPrime Taq HiFi (long denat., primer extension at 65°C). The coverage was plotted on a log 10 (a) and a linear scale (b). The data points at extremely high GC, where the reads from the PCR-free library had a mean base quality of less than Q20 (open symbols), were omitted in the middle panel (b). (c) The ratios of the two curves in (a,b), that is, the fold-increase in mean coverage by sequencing a PCR-free library instead of a PCR-amplified library. The shaded histogram is the %GC distribution of 50-bp windows in the human genome. More than 99.9% of all 50-bp windows in the genome contain 8% to 88% GC and received a less than 1.25-fold increase in coverage. Less than 0.01% of all 50-bp windows contain 90% or more GC. The open circles at 96% and 98% GC denote data for which the mean base quality of the reads from the PCR-free library was below Q20.

    Article Snippet: One unit of AccuPrime Taq DNA polymerase High Fidelity (Invitrogen) was used in 50 μl 1× AccuPrime PCR buffer II.

    Techniques: Sequencing, Polymerase Chain Reaction, Amplification

    Optimizing the PCR conditions . (a) Neither extending the denaturation times (dark red squares) nor adding 2M betaine (black triangles) is sufficient to recover extremely GC-rich DNA fragments by PCR with Phusion HF. (b) Combining long denaturation and 2M betaine is effective for the high-GC fraction (black triangles) but the profile is not as even over the entire GC spectrum as after PCR with AccuPrime Taq HiFi (blue diamonds) using extended denaturation times and a lower temperature (65°C) for primer annealing and extension.

    Journal: Genome Biology

    Article Title: Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

    doi: 10.1186/gb-2011-12-2-r18

    Figure Lengend Snippet: Optimizing the PCR conditions . (a) Neither extending the denaturation times (dark red squares) nor adding 2M betaine (black triangles) is sufficient to recover extremely GC-rich DNA fragments by PCR with Phusion HF. (b) Combining long denaturation and 2M betaine is effective for the high-GC fraction (black triangles) but the profile is not as even over the entire GC spectrum as after PCR with AccuPrime Taq HiFi (blue diamonds) using extended denaturation times and a lower temperature (65°C) for primer annealing and extension.

    Article Snippet: One unit of AccuPrime Taq DNA polymerase High Fidelity (Invitrogen) was used in 50 μl 1× AccuPrime PCR buffer II.

    Techniques: Polymerase Chain Reaction

    Confirmation of spy0129 Deletion Mutant and Adherence Assay Top panel is a schematic representation of the spy0127–0130 cluster. Position of primers for RT-PCR are indicated by arrows. (A) Results of RT-PCR analysis on mRNA from two putative deletion mutants (Δ1 and Δ2) and the parental SF370 strain (P). mRNA was isolated from mid log-phase or stationary phase cells (indicated below panel) and reverse-transcribed with two primer combinations, which are indicated at the top of the lanes as primer set A (0129F–0129R) and primer set B (0129F–0130R). cDNA products were separated on a 1% agarose gel and visualized by ethidium bromide staining. The expected sizes of resulting cDNAs from SF370 using primer set A is 365 bp and using primer set B is 1200 bp. Control reactions (C) containing mid-log phase mRNA and Taq DNA polymerase instead of reverse transcriptase are indicated. Lane 1 contains 1 kb Plus DNA ladder (1 μg; Invitrogen). (B) Results of the pharyngeal cell adherence assay (detailed in Methods), comparing parental strain SF370 to the spy0129–0130 isogenic mutant, SF370Δ spy0129 .2 (abbreviated as Δ spy0129 ). Adherent streptococci are reported as the percentage of total number of streptococci added as inoculum to pharyngeal cell monolayers. Statistical significance (reported as p -value) was determined by Student's t- test.

    Journal: PLoS Computational Biology

    Article Title: Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes

    doi: 10.1371/journal.pcbi.0030132

    Figure Lengend Snippet: Confirmation of spy0129 Deletion Mutant and Adherence Assay Top panel is a schematic representation of the spy0127–0130 cluster. Position of primers for RT-PCR are indicated by arrows. (A) Results of RT-PCR analysis on mRNA from two putative deletion mutants (Δ1 and Δ2) and the parental SF370 strain (P). mRNA was isolated from mid log-phase or stationary phase cells (indicated below panel) and reverse-transcribed with two primer combinations, which are indicated at the top of the lanes as primer set A (0129F–0129R) and primer set B (0129F–0130R). cDNA products were separated on a 1% agarose gel and visualized by ethidium bromide staining. The expected sizes of resulting cDNAs from SF370 using primer set A is 365 bp and using primer set B is 1200 bp. Control reactions (C) containing mid-log phase mRNA and Taq DNA polymerase instead of reverse transcriptase are indicated. Lane 1 contains 1 kb Plus DNA ladder (1 μg; Invitrogen). (B) Results of the pharyngeal cell adherence assay (detailed in Methods), comparing parental strain SF370 to the spy0129–0130 isogenic mutant, SF370Δ spy0129 .2 (abbreviated as Δ spy0129 ). Adherent streptococci are reported as the percentage of total number of streptococci added as inoculum to pharyngeal cell monolayers. Statistical significance (reported as p -value) was determined by Student's t- test.

    Article Snippet: RT–PCR generation of amplicons was performed with the SuperScript III One-Step RT–PCR system with Platinum Taq DNA polymerase (Invitrogen) in reaction mixtures (50 μl) containing 0.2 μM of each gene-specific forward and reverse primers and 0.1 μg of DNase-treated, purified total RNA from late-log phase cultures (OD = 0.7) of strain SF370.

    Techniques: Mutagenesis, Reverse Transcription Polymerase Chain Reaction, Isolation, Agarose Gel Electrophoresis, Staining

    Confirmation of speH Deletion Mutant and Pharyngeal Cell Adherence Assay (A) Results of RT-PCR and PCR analyses of total RNA preparations isolated from mid-log (OD = 0.4) and stationary phase (OD = 1) cultures of the ΔspeH deletion mutant (ΔL and ΔS, respectively), and stationary phase cultures of the SF370 parental strain (P). RNA was reverse-transcribed as described in Methods. To assess genomic DNA contamination, control reactions containing Taq DNA polymerase instead of reverse transcriptase were included. cDNA products were separated on a 1% agarose gel and visualized by ethidium bromide staining. Lanes containing products from either the RT-PCR or PCR analysis are designated at the bottom of the panel. Lanes labeled MW contain 1 kb Plus DNA ladder (1 μg; Invitrogen). (B) Results of the pharyngeal cell adherence assay (detailed in Methods), comparing parental strain SF370 with the deletion mutant SF370Δ speH (abbreviated Δ speH ). Adherent streptococci are reported as the percentage of total number of streptococci added as inoculum to pharyngeal cell monolayers. Statistical significance (reported as p value) was determined by Student's t- test.

    Journal: PLoS Computational Biology

    Article Title: Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes

    doi: 10.1371/journal.pcbi.0030132

    Figure Lengend Snippet: Confirmation of speH Deletion Mutant and Pharyngeal Cell Adherence Assay (A) Results of RT-PCR and PCR analyses of total RNA preparations isolated from mid-log (OD = 0.4) and stationary phase (OD = 1) cultures of the ΔspeH deletion mutant (ΔL and ΔS, respectively), and stationary phase cultures of the SF370 parental strain (P). RNA was reverse-transcribed as described in Methods. To assess genomic DNA contamination, control reactions containing Taq DNA polymerase instead of reverse transcriptase were included. cDNA products were separated on a 1% agarose gel and visualized by ethidium bromide staining. Lanes containing products from either the RT-PCR or PCR analysis are designated at the bottom of the panel. Lanes labeled MW contain 1 kb Plus DNA ladder (1 μg; Invitrogen). (B) Results of the pharyngeal cell adherence assay (detailed in Methods), comparing parental strain SF370 with the deletion mutant SF370Δ speH (abbreviated Δ speH ). Adherent streptococci are reported as the percentage of total number of streptococci added as inoculum to pharyngeal cell monolayers. Statistical significance (reported as p value) was determined by Student's t- test.

    Article Snippet: RT–PCR generation of amplicons was performed with the SuperScript III One-Step RT–PCR system with Platinum Taq DNA polymerase (Invitrogen) in reaction mixtures (50 μl) containing 0.2 μM of each gene-specific forward and reverse primers and 0.1 μg of DNase-treated, purified total RNA from late-log phase cultures (OD = 0.7) of strain SF370.

    Techniques: Mutagenesis, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Isolation, Agarose Gel Electrophoresis, Staining, Labeling

    PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of DNA polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with Taq DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.

    Journal: Nucleic Acids Research

    Article Title: Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance

    doi: 10.1093/nar/gkn575

    Figure Lengend Snippet: PAGE analysis of primer extension experiments with single OXP-modified and PDE primers. Primer extension with Klenow fragment of DNA polymerase I of nonheated ( A ) and preheated ( B ) single OXP-modified reverse primer, respectively along template 2. The extension reactions were incubated at 25°C for the indicated times after which the reaction mixtures were quenched and analyzed. ( C ) Primer extension with Taq DNA polymerase of PDE and OXP forward primers (nonheated control and preheated sample) along template oligonucleotide 1. Extension reactions were incubated at 25°C for 15 min, after which the aliquots from reaction mixtures were quenched and analyzed.

    Article Snippet: Primer extension with Taq DNA polymerase Primer extension experiments using recombinant Taq DNA polymerase (Invitrogen) were performed at 25°C using the OXP-modified forward primer and control PDE forward primer (5′-GAATTGGGTGTCAACATAGCAGAAT-3′).

    Techniques: Polyacrylamide Gel Electrophoresis, Modification, Incubation

    Comparison of the performance of OXP-modified primers to other Hot Start DNA polymerases. ( A ) Agarose gel analysis of the PCR products resulting from the 35 thermal cycles of amplification of five copies of a 365-bp fragment from the HIV-1 tat gene using 0.5 μM unmodified, single OXP-modified and double OXP-modified primers. Reactions containing unmodified primers were amplified by Taq DNA polymerase, Platinum® Taq DNA Polymerase, AmpliTaq Gold® DNA Polymerase, HotStart-IT™ Taq DNA Polymerase and DyNazyme™ II Hot Start DNA Polymerase. Reactions containing single and double OXP-modified primers were amplified by Taq DNA polymerase. ( B ) Graphical representation of PCR amplicon yield. The results from triplicate experiments were averaged and are normalized to the yield of reactions containing single OXP-modified primers plus Taq DNA polymerase. Error bars represent the SD. (*), indicates Hot Start DNA polymerases.

    Journal: Nucleic Acids Research

    Article Title: Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance

    doi: 10.1093/nar/gkn575

    Figure Lengend Snippet: Comparison of the performance of OXP-modified primers to other Hot Start DNA polymerases. ( A ) Agarose gel analysis of the PCR products resulting from the 35 thermal cycles of amplification of five copies of a 365-bp fragment from the HIV-1 tat gene using 0.5 μM unmodified, single OXP-modified and double OXP-modified primers. Reactions containing unmodified primers were amplified by Taq DNA polymerase, Platinum® Taq DNA Polymerase, AmpliTaq Gold® DNA Polymerase, HotStart-IT™ Taq DNA Polymerase and DyNazyme™ II Hot Start DNA Polymerase. Reactions containing single and double OXP-modified primers were amplified by Taq DNA polymerase. ( B ) Graphical representation of PCR amplicon yield. The results from triplicate experiments were averaged and are normalized to the yield of reactions containing single OXP-modified primers plus Taq DNA polymerase. Error bars represent the SD. (*), indicates Hot Start DNA polymerases.

    Article Snippet: Primer extension with Taq DNA polymerase Primer extension experiments using recombinant Taq DNA polymerase (Invitrogen) were performed at 25°C using the OXP-modified forward primer and control PDE forward primer (5′-GAATTGGGTGTCAACATAGCAGAAT-3′).

    Techniques: Modification, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification

    Dependence of pre-PCR heating of PTE on primer dimer accumulation. Agarose gel analysis of primer dimer accumulation with preheated single OXP-modified primers in nontemplate system. Mixture of both primers was preheated at 95°C in 1× PCR buffer (pH 8.4 at 25°C) for increasing amounts of time. Samples were cooled on ice water, the Taq DNA polymerase was added followed by PCR amplification. PCR cycle parameters: 95°C (2 min); 30 cycles of [95°C (40 s); 56°C (30 s); and 72°C (2 min)]; 72°C (7 min). Primer dimer amplicon, indicated on the gel image, ran as a 50–80 bp DNA fragment (left lane: 50-bp ladder).

    Journal: Nucleic Acids Research

    Article Title: Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance

    doi: 10.1093/nar/gkn575

    Figure Lengend Snippet: Dependence of pre-PCR heating of PTE on primer dimer accumulation. Agarose gel analysis of primer dimer accumulation with preheated single OXP-modified primers in nontemplate system. Mixture of both primers was preheated at 95°C in 1× PCR buffer (pH 8.4 at 25°C) for increasing amounts of time. Samples were cooled on ice water, the Taq DNA polymerase was added followed by PCR amplification. PCR cycle parameters: 95°C (2 min); 30 cycles of [95°C (40 s); 56°C (30 s); and 72°C (2 min)]; 72°C (7 min). Primer dimer amplicon, indicated on the gel image, ran as a 50–80 bp DNA fragment (left lane: 50-bp ladder).

    Article Snippet: Primer extension with Taq DNA polymerase Primer extension experiments using recombinant Taq DNA polymerase (Invitrogen) were performed at 25°C using the OXP-modified forward primer and control PDE forward primer (5′-GAATTGGGTGTCAACATAGCAGAAT-3′).

    Techniques: Polymerase Chain Reaction, Agarose Gel Electrophoresis, Modification, Amplification

    Evaluation of thermolabile primers in one-step RT–PCR. For each gene of interest ( PBGD , ABCA-1 and β-actin ), the PCR primers were unmodified, single OXP-modified or double OXP-modified primers. RT utilized a polydT 18 primer. Reactions contained Taq DNA polymerase and M-MLV reverse transcriptase.

    Journal: Nucleic Acids Research

    Article Title: Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance

    doi: 10.1093/nar/gkn575

    Figure Lengend Snippet: Evaluation of thermolabile primers in one-step RT–PCR. For each gene of interest ( PBGD , ABCA-1 and β-actin ), the PCR primers were unmodified, single OXP-modified or double OXP-modified primers. RT utilized a polydT 18 primer. Reactions contained Taq DNA polymerase and M-MLV reverse transcriptase.

    Article Snippet: Primer extension with Taq DNA polymerase Primer extension experiments using recombinant Taq DNA polymerase (Invitrogen) were performed at 25°C using the OXP-modified forward primer and control PDE forward primer (5′-GAATTGGGTGTCAACATAGCAGAAT-3′).

    Techniques: Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Modification

    Dependencies of apparent rate of substrate binding by DNA polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – Taq polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)

    Journal: Biochemistry

    Article Title: Cooperation between Catalytic and DNA-binding Domains Enhances Thermostability and Supports DNA Synthesis at Higher Temperatures by Thermostable DNA Polymerases

    doi: 10.1021/bi2014807

    Figure Lengend Snippet: Dependencies of apparent rate of substrate binding by DNA polymerases on temperature. Panel A , (○- PTJ1, ●- PTJ2) – Taq polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2)

    Article Snippet: Taq DNA polymerase was purchased from Roche Applied Science (Indianapolis, IN), the Stoffel fragment of Taq DNA polymerase was obtained from Applied BioSystems (Foster City, CA), and Pfu DNA polymerase was from Stratagene Cloning Systems (La Jolla, CA).

    Techniques: Binding Assay

    Thermostability of chimeric DNA polymerases ( see Materials and Methods ). Panel A shows the stability of Taq polymerase chimeras with truncated C-terminal TopoV tails at 100°C in the presence of 1 M potassium glutamate and 1 M betaine: (○)

    Journal: Biochemistry

    Article Title: Cooperation between Catalytic and DNA-binding Domains Enhances Thermostability and Supports DNA Synthesis at Higher Temperatures by Thermostable DNA Polymerases

    doi: 10.1021/bi2014807

    Figure Lengend Snippet: Thermostability of chimeric DNA polymerases ( see Materials and Methods ). Panel A shows the stability of Taq polymerase chimeras with truncated C-terminal TopoV tails at 100°C in the presence of 1 M potassium glutamate and 1 M betaine: (○)

    Article Snippet: Taq DNA polymerase was purchased from Roche Applied Science (Indianapolis, IN), the Stoffel fragment of Taq DNA polymerase was obtained from Applied BioSystems (Foster City, CA), and Pfu DNA polymerase was from Stratagene Cloning Systems (La Jolla, CA).

    Techniques:

    Dependencies of DNA polymerase processivity on temperature. Panel A , (○- PTJ1, ●- PTJ2) – Taq polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2) – Klentaq. Panel

    Journal: Biochemistry

    Article Title: Cooperation between Catalytic and DNA-binding Domains Enhances Thermostability and Supports DNA Synthesis at Higher Temperatures by Thermostable DNA Polymerases

    doi: 10.1021/bi2014807

    Figure Lengend Snippet: Dependencies of DNA polymerase processivity on temperature. Panel A , (○- PTJ1, ●- PTJ2) – Taq polymerase; (△- PTJ1, ▲- PTJ2) – Stoffel Fragment; (◇- PTJ1, ◆- PTJ2) – Klentaq. Panel

    Article Snippet: Taq DNA polymerase was purchased from Roche Applied Science (Indianapolis, IN), the Stoffel fragment of Taq DNA polymerase was obtained from Applied BioSystems (Foster City, CA), and Pfu DNA polymerase was from Stratagene Cloning Systems (La Jolla, CA).

    Techniques:

    . Accumulation of the inactive conformations with temperature increase and dependencies of DNA binding rate constant on temperature for Taq polymerase and its fragments ( A, B ), chimeric polymerases

    Journal: Biochemistry

    Article Title: Cooperation between Catalytic and DNA-binding Domains Enhances Thermostability and Supports DNA Synthesis at Higher Temperatures by Thermostable DNA Polymerases

    doi: 10.1021/bi2014807

    Figure Lengend Snippet: . Accumulation of the inactive conformations with temperature increase and dependencies of DNA binding rate constant on temperature for Taq polymerase and its fragments ( A, B ), chimeric polymerases

    Article Snippet: Taq DNA polymerase was purchased from Roche Applied Science (Indianapolis, IN), the Stoffel fragment of Taq DNA polymerase was obtained from Applied BioSystems (Foster City, CA), and Pfu DNA polymerase was from Stratagene Cloning Systems (La Jolla, CA).

    Techniques: Binding Assay