amplitaq gold dna polymerase (Thermo Fisher)

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AmpliTaq Gold DNA Polymerase

Description:

AmpliTaq Gold DNA Polymerase is a chemically modified form of AmpliTaq DNA Polymerase requiring thermal activation. Features of this enzyme:• Automated chemical hot-start enzyme for increased specificity, sensitivity, and yield• Time-released thermal activation improves sensitivity in low copy number amplifications• Successful multiplex PCR saves time and reagents• Includes GeneAmp 10X PCR Gold Buffer with MgCl2Hot-start activationThe modified enzyme is provided in an inactive state. Upon thermal activation, the modifier is permanently released, regenerating active enzyme. The resulting hot-start PCR amplification provides increased sensitivity, specificity, and yield over conventional PCR techniques.Higher specificity, higher yieldAmpliTaq Gold DNA Polymerase can be activated partially or completely in a pre-PCR heat step, or can be allowed to activate slowly in a time-released manner during the denaturation steps of thermal cycling. With or without a limited up-front heat activation step, active enzyme is released slowly during thermal cycling to match template concentration and increase specificity. The yield of specific product increases because reactants are not wasted in the formation of unintended products. Because AmpliTaq Gold DNA Polymerase is a chemical hot-start enzyme, there is no worry of biological contamination.GeneAmp 10X PCR Gold Buffer is formulated to provide flexible, efficient activation of AmpliTaq Gold DNA Polymerase, resulting in a highly specific, robust PCR amplification. The ionic strength and the pH of GeneAmp 10X PCR Gold Buffer have been optimized to provide a wider activation temperature and time range when used in conjunction with AmpliTaq Gold DNA Polymerase.AmpliTaq Gold 360 DNA Polymerase for superior performanceAlso available is AmpliTaq Gold 360 DNA Polymerase for even better PCR performance. Compared to AmpliTaq Gold DNA Polymerase, AmpliTaq Gold 360 DNA Polymerase is purified by an additional proprietary separation process to eliminate contaminating bacterial DNA sequences from the enzyme preparation. When used with the enhanced 360 Gold Buffer, this ultra-pure enzyme, in addition to its hot-start capabilities, reduces false positive results, amplifies low-level target sequences, and promotes the amplification of a variety of templates. Also included with this product is a 360 GC Enhancer to work through challenging GC-rich templates.

Catalog Number:

4311806

Price:

None

Applications:

Hot Start PCR|PCR|PCR & Real-Time PCR|PCR Enzymes & Master Mixes

Size:

250 units

Category:

Proteins, Enzymes, & Peptides, PCR & Cloning Enzymes, PCR Enzymes & Kits

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Structured Review

Thermo Fisher amplitaq gold dna polymerase

Hot Start <t>DNA</t> polymerase evaluation in triplex one-step RT-PCR amplification of ABCA5, ABCA6 and ABCA7 targets . Reactions contained 0.82 μg of human trachea total RNA and an unmodified oligo(dT) 18 RT primer. The PCR primers were either unmodified, or contained CleanAmp™ Precision modifications. These reactions contained one of the following DNA polymerases: Taq , Platinum ® Taq , or <t>AmpliTaq</t> Gold ® and one of the following reverse transcriptases: M-MLV or SSIII. Reactions with M-MLV were incubated at 42°C, while reactions with SSIII were incubated at 55°C.

amplitaq gold dna polymerase - by Bioz Stars, 2019-10

99/100 stars

Images

1) Product Images from "Selective control of primer usage in multiplex one-step reverse transcription PCR"

Article Title: Selective control of primer usage in multiplex one-step reverse transcription PCR

Journal: BMC Molecular Biology

doi: 10.1186/1471-2199-10-113

Hot Start DNA polymerase evaluation in triplex one-step RT-PCR amplification of ABCA5, ABCA6 and ABCA7 targets . Reactions contained 0.82 μg of human trachea total RNA and an unmodified oligo(dT) 18 RT primer. The PCR primers were either unmodified, or contained CleanAmp™ Precision modifications. These reactions contained one of the following DNA polymerases: Taq , Platinum ® Taq , or AmpliTaq Gold ® and one of the following reverse transcriptases: M-MLV or SSIII. Reactions with M-MLV were incubated at 42°C, while reactions with SSIII were incubated at 55°C.

Figure Legend Snippet: Hot Start DNA polymerase evaluation in triplex one-step RT-PCR amplification of ABCA5, ABCA6 and ABCA7 targets . Reactions contained 0.82 μg of human trachea total RNA and an unmodified oligo(dT) 18 RT primer. The PCR primers were either unmodified, or contained CleanAmp™ Precision modifications. These reactions contained one of the following DNA polymerases: Taq , Platinum ® Taq , or AmpliTaq Gold ® and one of the following reverse transcriptases: M-MLV or SSIII. Reactions with M-MLV were incubated at 42°C, while reactions with SSIII were incubated at 55°C.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Amplification, Polymerase Chain Reaction, Incubation

2) Product Images from "Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance"

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

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkn575

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.

Figure Legend 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.

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

Methylation Sequencing:

Article Title: Prognostic Values of EPDR1 Hypermethylation and Its Inhibitory Function on Tumor Invasion in Colorectal Cancer
Article Snippet: Paragraph title: 4.11. Bisulfite Sequencing PCR (BSP) ... Briefly, bisulfite-modified DNA was prepared and used as the template for amplification of the EPDR1 gene promoter using AmpliTaq Gold® DNA Polymerase (Applied Biosystems, Carlsbad, CA, USA).

Clone Assay:

Article Title: Vif Substitution Enables Persistent Infection of Pig-Tailed Macaques by Human Immunodeficiency Virus Type 1
Article Snippet: Paragraph title: PCR cloning of HSIV-vif sequences from pig-tailed macaques. ... PCR amplification for both rounds was initiated at 95°C for 5 min; this was followed with 35 cycles of 95°C for 1 min, 60°C for 1 min, and 72°C for 1 min, with a final extension at 72°C for 10 min. For both gag and vif reactions, PCR was carried out using a 250 nM concentration of each primer and AmpliTaq Gold DNA polymerase and buffer (Applied Biosystems). env sequences were amplified with previously described primers , but with AmpliTaq Gold DNA polymerase and buffer (Applied Biosystems).

Article Title: Prognostic Values of EPDR1 Hypermethylation and Its Inhibitory Function on Tumor Invasion in Colorectal Cancer
Article Snippet: Briefly, bisulfite-modified DNA was prepared and used as the template for amplification of the EPDR1 gene promoter using AmpliTaq Gold® DNA Polymerase (Applied Biosystems, Carlsbad, CA, USA). .. The PCR products were subcloned into the TA cloning vector (Bioman Scientific, Taipei, Taiwan) and transformed into DH5α competent cells (Bioman Scientific).

Article Title: Reversal of epigenetic promoter silencing in Friedreich ataxia by a class I histone deacetylase inhibitor
Article Snippet: A total of 20–50 ng of each bisulfite-treated DNA was used for PCR amplification (forward primer: 5′-ATCTCCCTTAAATCAAAAATCCTAA-3′, reverse primer: 5′-GCTGCGGGATTCGGGTGAGGGTTTGG-3′) using AmpliTaq® Gold DNA polymerase (Applied Biosystems). .. Conversely, inaccessible cytosines, which remain unmethylated after GpC-MT treatment are converted via bisulfite treatment to uracil, i.e. read as T (denoted as black boxes in Figure ).

Amplification:

Article Title: Vif Substitution Enables Persistent Infection of Pig-Tailed Macaques by Human Immunodeficiency Virus Type 1
Article Snippet: Vif sequences were amplified with primers pol-4933 (5′-CAGGGACAGCAGAGATCCAGTTTG-3′) and vpr-5842 (5′-CTACTGGCTCCATTTCTTGCTCTC-3′) in round 1 and pol-4986 (5′-GAAAGGTGAAGGGGCAGTAGTAATAC-3′) and vpr-5666 (5′-GTTGTCCTAAGTTATGGAGCCATATC-3′) in round 2. .. PCR amplification for both rounds was initiated at 95°C for 5 min; this was followed with 35 cycles of 95°C for 1 min, 60°C for 1 min, and 72°C for 1 min, with a final extension at 72°C for 10 min. For both gag and vif reactions, PCR was carried out using a 250 nM concentration of each primer and AmpliTaq Gold DNA polymerase and buffer (Applied Biosystems). env sequences were amplified with previously described primers , but with AmpliTaq Gold DNA polymerase and buffer (Applied Biosystems). .. Each round of amplification was initiated at 94°C for 5 min, followed by 35 cycles of 94°C for 30 s, annealing for 30 s, and 72°C for 3 min. Annealing was performed at 45°C in the first round and 50°C in the second.

Article Title: Intelligent image-based in situ single-cell isolation
Article Snippet: Paragraph title: Direct amplification and sequencing of shDNA fragments from human cells ... In the first PCR, we used 10 µM shDNA-specific primer pair with a universal tag sequence, 1 × PCR buffer, 2.0 mM MgCl2 , 2.5 mM dNTPs, and 1 unit of AmpliTaq Gold DNA Polymerase (Thermo Fisher, Cat. No. 8080241).

Article Title: Pronuclear transfer in human embryos to prevent transmission of mitochondrial DNA disease
Article Snippet: Follicular cell and sperm genomic DNA, and whole genome amplified embryo DNA were analysed for 16 polymorphic microsatellite markers using the PowerPlex® 16 System (Promega). .. PCR reactions were carried out in a volume of 12.5μl containing 1ng of DNA, 1X Gold Star buffer, 1X PowerPlex® 16 primer pair mix and 2 units of AmpliTaq Gold DNA polymerase (Applied Biosystems).

Article Title: Complex virome in feces from Amerindian children in isolated Amazonian villages
Article Snippet: Reverse transcription was performed with SuperScript III reverse transcriptase (Thermo Fisher Scientific, Massachusetts, USA) using a primer with a random nonamer at the 3’ end (5’GCCGACTAATGCGTAGTCNNNNNNNNN) and the second strand DNA was synthetized using Klenow Fragment (New England Biolabs, Massachusetts, USA) . .. The cDNA and DNA was then amplified by PCR with 15 cycles using a primer with the fixed portion of the previous primer (5’GCCGACTAATGCGTAGTC) and AmpliTaq Gold DNA polymerase (Thermo Fisher Scientific, Massachusetts, USA) . .. The amplification products were used to prepare the libraries individually for each sample using the Nextera XT DNA Sample Preparation Kit (Illumina, California, USA) following the manufacturer’s instructions, with 15 cycles of PCR amplification and dual index barcoding.

Article Title: Prognostic Values of EPDR1 Hypermethylation and Its Inhibitory Function on Tumor Invasion in Colorectal Cancer
Article Snippet: BSP was performed as described previously [ ]. .. Briefly, bisulfite-modified DNA was prepared and used as the template for amplification of the EPDR1 gene promoter using AmpliTaq Gold® DNA Polymerase (Applied Biosystems, Carlsbad, CA, USA). .. The primers used for BSP are listed in .

Article Title: Effect of a diet containing folate and hazelnut oil capsule on the methylation level of the ADRB3 gene, lipid profile and oxidative stress in overweight or obese women
Article Snippet: DNA was isolated with a QIAamp DNA Mini kit (Qiagen, Valencia, CA, USA), and the DNA concentrations of the samples were determined using a Qubit® dsDNA HS Assay Kit. .. Genomic DNA was modified by bisulfite and amplified by AmpliTaq Gold® DNA Polymerase (Applied Biosystems, California 94404, USA) using the sequence described in Table . .. The PCR program consisted of an initial enzymatic activation at 95 °C for 10 min, followed by 50 cycles of 45 s at 95 °C, 45 s at 60 °C and 45 s at 72 °C and a final extension at 72 °C for 10 min.

Article Title: Reversal of epigenetic promoter silencing in Friedreich ataxia by a class I histone deacetylase inhibitor
Article Snippet: Briefly, cells were cross-linked and chromatin was treated with GpC methyltransferase (GpC-MT) and subjected to bisulfite conversion. .. A total of 20–50 ng of each bisulfite-treated DNA was used for PCR amplification (forward primer: 5′-ATCTCCCTTAAATCAAAAATCCTAA-3′, reverse primer: 5′-GCTGCGGGATTCGGGTGAGGGTTTGG-3′) using AmpliTaq® Gold DNA polymerase (Applied Biosystems). .. PCR products were TA-cloned using the TOPO TA Cloning® Kit (Invitrogen), transformed into competent Escherichia coli (DH5α) and individual clones were sequenced.

Article Title: Genomic analysis of liver cancer unveils novel driver genes and distinct prognostic features
Article Snippet: Complementary DNA was synthesized from total RNA using ABITM reverse transcription kit and (Applied Biosystems, Foster City, CA). .. For semi-quantitative reverse-transcription-PCR, AURKA and ACTB were amplified with AmpliTaq Gold DNA polymerase (Applied Biosystems) using the following primers: AURKA forward, 5′-GGAATATGCACCACTTGGAACA-3′; AURKA reverse, 5′-TAAGACAGGGCATTTGCCAAT-3′; ACTB forward, 5′-CATCCACGAAACTACCTTCAACTCC-3′; ACTB reverse, 5′-GAGCCGCCGATCCACACG-3′. .. Cell viability was assayed using 3-(4,5-dimethylthiazolyl)- 2,5-diphenyltetrazoliumbromide (MTT) assays (Sigma-Aldrich, Carlsbad, CA, USA).

Article Title: Molecular and serological characterization of hepatitis B vaccine breakthrough infections in serial samples from two plasma donors
Article Snippet: First- and second-round PCR were performed to amplify the preS1-S region using Amplitaq Gold® DNA polymerase (Applied Biosystems, Foster City, CA). .. The 50 μl PCR reaction contained 0.4 μM of each primer, 2.5 mM MgCl2, 0.8 μM dNTP mix and 25 μl extracted DNA for the first-round PCR, or 2 μl of the first-round PCR as a template for the second-round.

Whole Genome Amplification:

Article Title: Pronuclear transfer in human embryos to prevent transmission of mitochondrial DNA disease
Article Snippet: Whole genome amplification from 4 individual embryos cultured to the 2-8-cell stage, was performed using the REPLI-g® Mini kit (Qiagen, Crawley, UK). .. PCR reactions were carried out in a volume of 12.5μl containing 1ng of DNA, 1X Gold Star buffer, 1X PowerPlex® 16 primer pair mix and 2 units of AmpliTaq Gold DNA polymerase (Applied Biosystems).

Synthesized:

TA Cloning:

Article Title: Prognostic Values of EPDR1 Hypermethylation and Its Inhibitory Function on Tumor Invasion in Colorectal Cancer
Article Snippet: Briefly, bisulfite-modified DNA was prepared and used as the template for amplification of the EPDR1 gene promoter using AmpliTaq Gold® DNA Polymerase (Applied Biosystems, Carlsbad, CA, USA). .. Briefly, bisulfite-modified DNA was prepared and used as the template for amplification of the EPDR1 gene promoter using AmpliTaq Gold® DNA Polymerase (Applied Biosystems, Carlsbad, CA, USA).

Real-time Polymerase Chain Reaction:

Article Title: Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance
Article Snippet: AmpliTaq Gold® DNA Polymerase was purchased from Applied Biosystems and HotStart-IT® Taq DNA polymerase was purchased from USB (Cleveland, OH, USA). .. All endpoint PCR experiments were performed on either a Perkin Elmer GeneAmp® 9600 or a Perkin Elmer GeneAmp® 2400 thermal cycler.

Incubation:

Article Title: Intelligent image-based in situ single-cell isolation
Article Snippet: After capture, we added 0.5 µl Proteinase K (1 mg/ml) to the samples and incubated them at 60 ˚C for 20 min, followed by 3 min at 98 ˚C. .. In the first PCR, we used 10 µM shDNA-specific primer pair with a universal tag sequence, 1 × PCR buffer, 2.0 mM MgCl2 , 2.5 mM dNTPs, and 1 unit of AmpliTaq Gold DNA Polymerase (Thermo Fisher, Cat. No. 8080241).

Article Title: Complex virome in feces from Amerindian children in isolated Amazonian villages
Article Snippet: The filtrate was incubated with DNase and RNase enzymes (Turbo DNase, Thermo Fisher Scientific, Massachusetts, USA; Baseline Zero DNase, Epicentre, Wisconsin, USA; Benzonase Nuclease, Novagen, Massachusetts, USA; and RNase A, Thermo Fisher Scientific) at 37 °C for 90 min to degrade unprotected nucleic acid . .. The cDNA and DNA was then amplified by PCR with 15 cycles using a primer with the fixed portion of the previous primer (5’GCCGACTAATGCGTAGTC) and AmpliTaq Gold DNA polymerase (Thermo Fisher Scientific, Massachusetts, USA) .

Mass Spectrometry:

Article Title: Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance
Article Snippet: Electrospray mass spectrometry analyses were done by HT Laboratories (San Diego, CA, USA). .. AmpliTaq Gold® DNA Polymerase was purchased from Applied Biosystems and HotStart-IT® Taq DNA polymerase was purchased from USB (Cleveland, OH, USA).

Article Title: Low prevalence of Merkel cell polyomavirus in human epithelial thymic tumors
Article Snippet: PCR was performed with 250 ng of genomic DNA using the AmpliTaq Gold DNA Polymerase (Thermo Fisher Scientific, Naarden, The Netherlands) in a final volume of 50 μL, as recently described. .. DNA quality and integrity were assessed by specimen control size ladder (SCS) as previously described and published for the DNA used., All gained PCR fragments were confirmed by sequencing.

Modification:

Transformation Assay:

Article Title: Prognostic Values of EPDR1 Hypermethylation and Its Inhibitory Function on Tumor Invasion in Colorectal Cancer
Article Snippet: Briefly, bisulfite-modified DNA was prepared and used as the template for amplification of the EPDR1 gene promoter using AmpliTaq Gold® DNA Polymerase (Applied Biosystems, Carlsbad, CA, USA). .. Briefly, bisulfite-modified DNA was prepared and used as the template for amplification of the EPDR1 gene promoter using AmpliTaq Gold® DNA Polymerase (Applied Biosystems, Carlsbad, CA, USA).

Sampling:

Article Title: Effect of a diet containing folate and hazelnut oil capsule on the methylation level of the ADRB3 gene, lipid profile and oxidative stress in overweight or obese women
Article Snippet: Genomic DNA was modified by bisulfite and amplified by AmpliTaq Gold® DNA Polymerase (Applied Biosystems, California 94404, USA) using the sequence described in Table . .. Genomic DNA was modified by bisulfite and amplified by AmpliTaq Gold® DNA Polymerase (Applied Biosystems, California 94404, USA) using the sequence described in Table .

Diagnostic Assay:

Article Title: Effect of a diet containing folate and hazelnut oil capsule on the methylation level of the ADRB3 gene, lipid profile and oxidative stress in overweight or obese women
Article Snippet: Genomic DNA was modified by bisulfite and amplified by AmpliTaq Gold® DNA Polymerase (Applied Biosystems, California 94404, USA) using the sequence described in Table . .. Genomic DNA was modified by bisulfite and amplified by AmpliTaq Gold® DNA Polymerase (Applied Biosystems, California 94404, USA) using the sequence described in Table .

Cell Culture:

Reverse Transcription Polymerase Chain Reaction:

Article Title: Selective control of primer usage in multiplex one-step reverse transcription PCR
Article Snippet: Paragraph title: One-step RT-PCR (Endpoint) ... Reaction conditions included 1× PCR buffer (20 mM Tris (pH 8.4), 50 mM KCl) (Invitrogen), 1.5 mM MgCl2 (Invitrogen), gene-specific PCR primers (0.5 μM) (TriLink), oligo(dT)18 primer (1 μM) (TriLink), 0.16 mM dNTPs (New England Biolabs), 0.5 μL of human trachea total RNA or other human total RNA (Stratagene or Ambion, each at ~1.6 μg/μL), 5 U RNase Inhibitor (New England Biolabs), 50 U Moloney Murine Leukemia Virus Reverse Transcriptase (M-MLV RT) (Invitrogen) or SuperScript® III Reverse Transcriptase (SSIII RT) (Invitrogen), and 0.6 U of Taq DNA Polymerase, recombinant (Invitrogen) or Platinum® Taq DNA Polymerase (Invitrogen) or AmpliTaq Gold® DNA Polymerase (Applied Biosystems), in a 50 μL reaction volume.

Article Title: Integrative Analysis Revealing Human Adipose-Specific Genes and Consolidating Obesity Loci
Article Snippet: Paragraph title: Semi-quantitative RT-PCR ... Exactly 1 µL of cDNA samples was used as a template for PCR in a 25 µL total reaction with AmpliTaq Gold DNA polymerase (Applied Biosystems, Carlsbad, CA).

Sequencing:

Article Title: Intelligent image-based in situ single-cell isolation
Article Snippet: Next, a two-step amplification reaction was carried out in 20 µl volume. .. In the first PCR, we used 10 µM shDNA-specific primer pair with a universal tag sequence, 1 × PCR buffer, 2.0 mM MgCl2 , 2.5 mM dNTPs, and 1 unit of AmpliTaq Gold DNA Polymerase (Thermo Fisher, Cat. No. 8080241). .. In the second PCR, 1 µl from the first amplification reaction was used as a template with primers complementary to the universal tag sequence.

Article Title: Complex virome in feces from Amerindian children in isolated Amazonian villages
Article Snippet: Paragraph title: Viral nucleic acid isolation and sequencing ... The cDNA and DNA was then amplified by PCR with 15 cycles using a primer with the fixed portion of the previous primer (5’GCCGACTAATGCGTAGTC) and AmpliTaq Gold DNA polymerase (Thermo Fisher Scientific, Massachusetts, USA) .

Article Title: Reversal of epigenetic promoter silencing in Friedreich ataxia by a class I histone deacetylase inhibitor
Article Snippet: Paragraph title: Nucleosome occupancy and Methylome sequencing (NOMe-Seq) ... A total of 20–50 ng of each bisulfite-treated DNA was used for PCR amplification (forward primer: 5′-ATCTCCCTTAAATCAAAAATCCTAA-3′, reverse primer: 5′-GCTGCGGGATTCGGGTGAGGGTTTGG-3′) using AmpliTaq® Gold DNA polymerase (Applied Biosystems).

Article Title: TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer
Article Snippet: Paragraph title: Mutation validation with Sanger sequencing ... PCR was carried out using AmpliTaq Gold DNA Polymerase (Applied Biosystems) based on the standard protocol.

Article Title: Molecular and serological characterization of hepatitis B vaccine breakthrough infections in serial samples from two plasma donors
Article Snippet: Paragraph title: Sequencing of the PreS1-PreS2-S gene region ... First- and second-round PCR were performed to amplify the preS1-S region using Amplitaq Gold® DNA polymerase (Applied Biosystems, Foster City, CA).

Recombinant:

Article Title: Selective control of primer usage in multiplex one-step reverse transcription PCR
Article Snippet: A one-step RT-PCR protocol was used in which the components were combined in a single tube. .. Reaction conditions included 1× PCR buffer (20 mM Tris (pH 8.4), 50 mM KCl) (Invitrogen), 1.5 mM MgCl2 (Invitrogen), gene-specific PCR primers (0.5 μM) (TriLink), oligo(dT)18 primer (1 μM) (TriLink), 0.16 mM dNTPs (New England Biolabs), 0.5 μL of human trachea total RNA or other human total RNA (Stratagene or Ambion, each at ~1.6 μg/μL), 5 U RNase Inhibitor (New England Biolabs), 50 U Moloney Murine Leukemia Virus Reverse Transcriptase (M-MLV RT) (Invitrogen) or SuperScript® III Reverse Transcriptase (SSIII RT) (Invitrogen), and 0.6 U of Taq DNA Polymerase, recombinant (Invitrogen) or Platinum® Taq DNA Polymerase (Invitrogen) or AmpliTaq Gold® DNA Polymerase (Applied Biosystems), in a 50 μL reaction volume. .. Thermal cycling conditions utilized a reverse transcription step at 42°C for 30 min when M-MLV RT was used and 55°C for 30 min when SSIII RT was employed; 95°C for 10 min (RT inactivation and initial denaturation step), followed by 45 PCR cycles at 95°C for 30 sec, 60°C for 1 min and final extension at 72°C for 5 min.

Article Title: Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance
Article Snippet: Thermus aquaticus (Taq ) DNA polymerase (recombinant) and Platinum® Taq DNA Polymerases were purchased from Invitrogen (Carlsbad, CA, USA). .. AmpliTaq Gold® DNA Polymerase was purchased from Applied Biosystems and HotStart-IT® Taq DNA polymerase was purchased from USB (Cleveland, OH, USA).

Methylation:

Article Title: Effect of a diet containing folate and hazelnut oil capsule on the methylation level of the ADRB3 gene, lipid profile and oxidative stress in overweight or obese women
Article Snippet: Paragraph title: Methylation levels ... Genomic DNA was modified by bisulfite and amplified by AmpliTaq Gold® DNA Polymerase (Applied Biosystems, California 94404, USA) using the sequence described in Table .

Article Title: Reversal of epigenetic promoter silencing in Friedreich ataxia by a class I histone deacetylase inhibitor
Article Snippet: A total of 20–50 ng of each bisulfite-treated DNA was used for PCR amplification (forward primer: 5′-ATCTCCCTTAAATCAAAAATCCTAA-3′, reverse primer: 5′-GCTGCGGGATTCGGGTGAGGGTTTGG-3′) using AmpliTaq® Gold DNA polymerase (Applied Biosystems). .. PCR products were TA-cloned using the TOPO TA Cloning® Kit (Invitrogen), transformed into competent Escherichia coli (DH5α) and individual clones were sequenced.

Mutagenesis:

Isolation:

Article Title: Vif Substitution Enables Persistent Infection of Pig-Tailed Macaques by Human Immunodeficiency Virus Type 1
Article Snippet: The sequences of HSIV-vif gag , vif , env , and nef were amplified by nested PCR from DNA isolated from PBMC by using a QIAamp DNA minikit (Qiagen). .. PCR amplification for both rounds was initiated at 95°C for 5 min; this was followed with 35 cycles of 95°C for 1 min, 60°C for 1 min, and 72°C for 1 min, with a final extension at 72°C for 10 min. For both gag and vif reactions, PCR was carried out using a 250 nM concentration of each primer and AmpliTaq Gold DNA polymerase and buffer (Applied Biosystems). env sequences were amplified with previously described primers , but with AmpliTaq Gold DNA polymerase and buffer (Applied Biosystems).

Purification:

Article Title: A novel variant of torque teno virus 7 identified in patients with Kawasaki disease
Article Snippet: All PCR amplifications were performed in a 12.5 μl cocktail containing 1–2 μl genomic DNA, 0.25 μl of each primer (10 μM), 1.25 μl of 10× PCR Buffer containing 15 mM MgCl2 , 1.25 μl of 2 mM dNTP mixture, and 0.125 μl AmpliTaq Gold DNA Polymerase (Thermo Fisher Scientific, Waltham, MA). .. All PCR amplifications were performed in a 12.5 μl cocktail containing 1–2 μl genomic DNA, 0.25 μl of each primer (10 μM), 1.25 μl of 10× PCR Buffer containing 15 mM MgCl2 , 1.25 μl of 2 mM dNTP mixture, and 0.125 μl AmpliTaq Gold DNA Polymerase (Thermo Fisher Scientific, Waltham, MA).

Article Title: Molecular and serological characterization of hepatitis B vaccine breakthrough infections in serial samples from two plasma donors
Article Snippet: First- and second-round PCR were performed to amplify the preS1-S region using Amplitaq Gold® DNA polymerase (Applied Biosystems, Foster City, CA). .. The 50 μl PCR reaction contained 0.4 μM of each primer, 2.5 mM MgCl2, 0.8 μM dNTP mix and 25 μl extracted DNA for the first-round PCR, or 2 μl of the first-round PCR as a template for the second-round.

Polymerase Chain Reaction:

Article Title: Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance
Article Snippet: AmpliTaq Gold® DNA Polymerase was purchased from Applied Biosystems and HotStart-IT® Taq DNA polymerase was purchased from USB (Cleveland, OH, USA). .. AmpliTaq Gold® DNA Polymerase was purchased from Applied Biosystems and HotStart-IT® Taq DNA polymerase was purchased from USB (Cleveland, OH, USA).

Article Title: Low prevalence of Merkel cell polyomavirus in human epithelial thymic tumors
Article Snippet: All use of this tissue and patient data was in agreement with the Dutch Code of Conduct for Observational Research with Personal Data (2004) and Tissue (2011, www.federa.org/sites/default/files/digital_ version_first_part_code_of_conduct_in_uk_2011_12092012.pdf ). .. PCR was performed with 250 ng of genomic DNA using the AmpliTaq Gold DNA Polymerase (Thermo Fisher Scientific, Naarden, The Netherlands) in a final volume of 50 μL, as recently described. .. DNA quality and integrity were assessed by specimen control size ladder (SCS) as previously described and published for the DNA used., All gained PCR fragments were confirmed by sequencing.

Article Title: TP53 R72P polymorphism modulates DNA methylation in hepatocellular carcinoma
Article Snippet: The methylation index (MethIndex) was defined as the ratio of the number of loci found methylated (Met(+)Loci ) on the total number of informative loci in a given sample([Met(+) + Met(−)]Loci ): Met(+)-Loci÷[Met(+) + Met(−)]Loci . .. Each PCR reaction was performed in a 25 μl final volume containing 100 ng of genomic DNA, 1X PCR buffer, 1.5 mM MgCl2 , 200 mMdNTP, 20 pmol of each primer, 5 units of AmpliTaq GOLD DNA polymerase (Applied Biosystem, Saint-Aubin, France). .. Reactions were subjected to 94°C for 5 min, followed by 40 cycles at 95°C for 1 min, 50-60°C for 1 min and 72°C for 1 min and final extension at 72°C for 7 min on a MyCycler thermal cycler (Bio-Rad, Marnes-la-Coquette, France).

Article Title: Integrative Analysis Revealing Human Adipose-Specific Genes and Consolidating Obesity Loci
Article Snippet: The thermal cycle of reverse transcription (RT) was 65 °C for 5 min, 37 °C for 52 min, and 70 °C for 15 min. .. Exactly 1 µL of cDNA samples was used as a template for PCR in a 25 µL total reaction with AmpliTaq Gold DNA polymerase (Applied Biosystems, Carlsbad, CA). .. The conditions for this reaction were 95 °C for 10 min, appropriate cycles with linear amplification ranges of 94 °C for 30 s, 55 °C for 30 s, 72 °C for 30 s, with an additional extension step at 72 °C for 10 min. PCR products were separated by using 1% agarose gel electrophoresis.

Article Title: Production of Cloned Miniature Pigs Expressing High Levels of Human Apolipoprotein(a) in Plasma
Article Snippet: We genotyped 12 microsatellite markers on the USDA swine linkage maps: S0038, S0091, S0227, SW1378, SW1434, SW1681, SW1954, SW2108, SW2494, SWR153, SWR1941, and TNFB [ ]. .. PCR was performed using AmpliTaq Gold DNA polymerase (Applied Biosystems, Tokyo, Japan). .. Amplified DNA fragments were electrophoresed using an ABI 3100 genetic analyzer.

Article Title: TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer
Article Snippet: Primer sets for polymerase chain reaction (PCR) were designed using the design tool Oligo 6.0. .. PCR was carried out using AmpliTaq Gold DNA Polymerase (Applied Biosystems) based on the standard protocol. .. Amplicons from target genes in 16 tumors were amplified (Supplementary Table S4).

Article Title: A novel variant of torque teno virus 7 identified in patients with Kawasaki disease
Article Snippet: To genotype rs2254546 and rs2736340 in the BLK [ , ], as well as rs28493229 in the ITPKC [ ], we obtained a DNA fragment of 480 base pairs containing rs2254546 and rs2736340 and another fragment of 202 base pairs containing rs28493229 by PCR using the following two primer sets, respectively: 5’-CCACGGAGAAAACTGCTGGA-3’ (forward primer) and 5’-AGAGGTGCCATTTCTGGGTG-3’ (reverse primer); 5’-GAGTCTGAGGATGACGTGGTG-3’ (forward primer) and 5’-CAGTGGATGGAAGAGGTTCCC-3’ (reverse primer). .. All PCR amplifications were performed in a 12.5 μl cocktail containing 1–2 μl genomic DNA, 0.25 μl of each primer (10 μM), 1.25 μl of 10× PCR Buffer containing 15 mM MgCl2 , 1.25 μl of 2 mM dNTP mixture, and 0.125 μl AmpliTaq Gold DNA Polymerase (Thermo Fisher Scientific, Waltham, MA). .. The following cycling conditions were used: pre-incubation at 95°C for 10 minutes; 35 cycles of 30 seconds at 95°C, 30 seconds at 58°C, and 30 seconds at 72°C; and final extension for 7 minutes at 72°C.

Article Title: Molecular and serological characterization of hepatitis B vaccine breakthrough infections in serial samples from two plasma donors
Article Snippet: HBV DNA was extracted from 0.5 mL of plasma using an automated DNA sample preparation protocol DNA-protK-500-50 (research use only) on the m 2000sp system (Abbott Molecular, Des Plaines, IL). .. First- and second-round PCR were performed to amplify the preS1-S region using Amplitaq Gold® DNA polymerase (Applied Biosystems, Foster City, CA). .. The first-round primers were HBV2813F (5′- TCATTTTGTGGGTCACCATATT-3′, nt 2811–2832) and 18R (5′-CCCATGAAGTTTAGGGAATAAC-3′, nt 860–881); the second-round primers were HBV-2822F (5′- GGGTCACCATATTCTTGGGAAC-3′, nt 2820–2841) and 19R (5′- GTTAGGGTTTAAATGTATACCC-3′, nt 822–843) amplifying a 1245 base pair fragment.

Metabolic Labelling:

Article Title: Effect of a diet containing folate and hazelnut oil capsule on the methylation level of the ADRB3 gene, lipid profile and oxidative stress in overweight or obese women
Article Snippet: Genomic DNA was modified by bisulfite and amplified by AmpliTaq Gold® DNA Polymerase (Applied Biosystems, California 94404, USA) using the sequence described in Table . .. Genomic DNA was modified by bisulfite and amplified by AmpliTaq Gold® DNA Polymerase (Applied Biosystems, California 94404, USA) using the sequence described in Table .

Staining:

Article Title: TP53 R72P polymorphism modulates DNA methylation in hepatocellular carcinoma
Article Snippet: Each PCR reaction was performed in a 25 μl final volume containing 100 ng of genomic DNA, 1X PCR buffer, 1.5 mM MgCl2 , 200 mMdNTP, 20 pmol of each primer, 5 units of AmpliTaq GOLD DNA polymerase (Applied Biosystem, Saint-Aubin, France). .. Each PCR reaction was performed in a 25 μl final volume containing 100 ng of genomic DNA, 1X PCR buffer, 1.5 mM MgCl2 , 200 mMdNTP, 20 pmol of each primer, 5 units of AmpliTaq GOLD DNA polymerase (Applied Biosystem, Saint-Aubin, France).

Nested PCR:

Agarose Gel Electrophoresis:

Article Title: Intelligent image-based in situ single-cell isolation
Article Snippet: In the first PCR, we used 10 µM shDNA-specific primer pair with a universal tag sequence, 1 × PCR buffer, 2.0 mM MgCl2 , 2.5 mM dNTPs, and 1 unit of AmpliTaq Gold DNA Polymerase (Thermo Fisher, Cat. No. 8080241). .. Other PCR conditions were the same as the first ones performing 30 PCR cycles this time.

Plasmid Preparation:

Article Title: Prognostic Values of EPDR1 Hypermethylation and Its Inhibitory Function on Tumor Invasion in Colorectal Cancer
Article Snippet: Briefly, bisulfite-modified DNA was prepared and used as the template for amplification of the EPDR1 gene promoter using AmpliTaq Gold® DNA Polymerase (Applied Biosystems, Carlsbad, CA, USA). .. Briefly, bisulfite-modified DNA was prepared and used as the template for amplification of the EPDR1 gene promoter using AmpliTaq Gold® DNA Polymerase (Applied Biosystems, Carlsbad, CA, USA).

Software:

Article Title: Pronuclear transfer in human embryos to prevent transmission of mitochondrial DNA disease
Article Snippet: PCR reactions were carried out in a volume of 12.5μl containing 1ng of DNA, 1X Gold Star buffer, 1X PowerPlex® 16 primer pair mix and 2 units of AmpliTaq Gold DNA polymerase (Applied Biosystems). .. PCR reactions were carried out in a volume of 12.5μl containing 1ng of DNA, 1X Gold Star buffer, 1X PowerPlex® 16 primer pair mix and 2 units of AmpliTaq Gold DNA polymerase (Applied Biosystems).

Article Title: Effect of a diet containing folate and hazelnut oil capsule on the methylation level of the ADRB3 gene, lipid profile and oxidative stress in overweight or obese women
Article Snippet: Genomic DNA was modified by bisulfite and amplified by AmpliTaq Gold® DNA Polymerase (Applied Biosystems, California 94404, USA) using the sequence described in Table . .. The PCR program consisted of an initial enzymatic activation at 95 °C for 10 min, followed by 50 cycles of 45 s at 95 °C, 45 s at 60 °C and 45 s at 72 °C and a final extension at 72 °C for 10 min.

Article Title: TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer
Article Snippet: PCR was carried out using AmpliTaq Gold DNA Polymerase (Applied Biosystems) based on the standard protocol. .. The cleaned products were mixed with 5 pmol of the forward or reverse PCR primers for sequencing.

Article Title: Molecular and serological characterization of hepatitis B vaccine breakthrough infections in serial samples from two plasma donors
Article Snippet: First- and second-round PCR were performed to amplify the preS1-S region using Amplitaq Gold® DNA polymerase (Applied Biosystems, Foster City, CA). .. First- and second-round PCR were performed to amplify the preS1-S region using Amplitaq Gold® DNA polymerase (Applied Biosystems, Foster City, CA).

RNA Extraction:

Article Title: Genomic analysis of liver cancer unveils novel driver genes and distinct prognostic features
Article Snippet: Paragraph title: RNA extraction and semi-quantitative reverse-transcription-PCR ... For semi-quantitative reverse-transcription-PCR, AURKA and ACTB were amplified with AmpliTaq Gold DNA polymerase (Applied Biosystems) using the following primers: AURKA forward, 5′-GGAATATGCACCACTTGGAACA-3′; AURKA reverse, 5′-TAAGACAGGGCATTTGCCAAT-3′; ACTB forward, 5′-CATCCACGAAACTACCTTCAACTCC-3′; ACTB reverse, 5′-GAGCCGCCGATCCACACG-3′.

Sample Prep:

Gel Permeation Chromatography:

Nuclear Magnetic Resonance:

Article Title: Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance
Article Snippet: NMR spectra were recorded on Bruker Model AX 500 spectrometer (NuMega, San Diego, CA, USA). .. AmpliTaq Gold® DNA Polymerase was purchased from Applied Biosystems and HotStart-IT® Taq DNA polymerase was purchased from USB (Cleveland, OH, USA).

Spectrophotometry:

Article Title: Integrative Analysis Revealing Human Adipose-Specific Genes and Consolidating Obesity Loci
Article Snippet: To measure the quantity of RNA, a Nanodrop spectrophotometer (Thermo Scientific, Wilmington, DE) was used. .. Exactly 1 µL of cDNA samples was used as a template for PCR in a 25 µL total reaction with AmpliTaq Gold DNA polymerase (Applied Biosystems, Carlsbad, CA).

DNA Methylation Assay:

Article Title: Effect of a diet containing folate and hazelnut oil capsule on the methylation level of the ADRB3 gene, lipid profile and oxidative stress in overweight or obese women
Article Snippet: DNA methylation in genomic DNA from blood was quantified at the CarMeN/Université de Lyon1-France Laboratory. .. Genomic DNA was modified by bisulfite and amplified by AmpliTaq Gold® DNA Polymerase (Applied Biosystems, California 94404, USA) using the sequence described in Table .

Concentration Assay:

Marker:

Article Title: Production of Cloned Miniature Pigs Expressing High Levels of Human Apolipoprotein(a) in Plasma
Article Snippet: Paragraph title: Microsatellite marker analysis ... PCR was performed using AmpliTaq Gold DNA polymerase (Applied Biosystems, Tokyo, Japan).

Lysis:

Article Title: Pronuclear transfer in human embryos to prevent transmission of mitochondrial DNA disease
Article Snippet: Lysis was terminated with 2.5μl 200mM Tricine. .. PCR reactions were carried out in a volume of 12.5μl containing 1ng of DNA, 1X Gold Star buffer, 1X PowerPlex® 16 primer pair mix and 2 units of AmpliTaq Gold DNA polymerase (Applied Biosystems).

amplitaq gold dna polymerase