phusion high fidelity dna polymerase  (Thermo Fisher)


Bioz Verified Symbol Thermo Fisher is a verified supplier
Bioz Manufacturer Symbol Thermo Fisher manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 86
    Name:
    Phusion High Fidelity DNA Polymerase
    Description:

    Catalog Number:
    f-530l
    Price:
    None
    Buy from Supplier


    Structured Review

    Thermo Fisher phusion high fidelity dna polymerase

    https://www.bioz.com/result/phusion high fidelity dna polymerase/product/Thermo Fisher
    Average 86 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    phusion high fidelity dna polymerase - by Bioz Stars, 2021-03
    86/100 stars

    Images

    Related Articles

    Polymerase Chain Reaction:

    Article Title: Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes
    Article Snippet: From a single pool of adapter-ligated library, aliquots were amplified using standard Illumina PCR reagents or using various alternative polymerases under optimized PCR conditions. .. Standard Illumina PCR (50 μl) with Phusion polymerase (Thermo) contained 1× Phusion DNA polymerase master mix and 0.4 μM of each primer pair and was amplified with thermocycling conditions of 1 min at 98°C for the initial denaturation, followed by 12 cycles of [10 s at 98°C, 30 s at 65°C, 30 s at 72°C] and a final extension for 5 min at 72°C. .. PCR (50 μl) with Kapa HiFi (KAPA Biosystems, South Africa) contained 1× Kapa HiFi buffer (containing TMAC) or 1× Kapa buffer B, 0.3 mM of each dNTP, 0.4 μM of each primer pair, 1 unit of Kapa HiFi and was amplified with thermocycling conditions of 1 min at 98°C for the initial denaturation followed by 12 cycles of [10 s at 98°C, 1 min at 65°C] and a final extension for 5 min at 65°C.

    Article Title: Improvement of long segment ribosomal PCR amplification for molecular identification of Litylenchus crenatae mccannii associated with beech leaf disease
    Article Snippet: .. Phusion™ High-Fidelity DNA polymeraseEach PCR amplification with Phusion™ High-Fidelity DNA Polymerase (Thermo Fisher Scientific, Waltham, MA) was carried out in a 25 μl of mixture containing Phusion™ High-Fidelity DNA Polymerase (2 units/μl) 0.25 μl, 5× reaction buffer 5 μl, dNTP (2.5 mM each) 0.5 μl, Template DNA 2 μl, forward primer 18S-CL-F3 (10 μm) 1.25 μl, reverse primer 28S-CL-R (10 μm) 1.25 μl, DMSO 0.25 μl, and molecular biology grade water (Sigma-Aldrich, St Louis, MO) 14.5 μl. ..

    Article Title: The occurrence and formation of monoterpenes in herbivore-damaged poplar roots
    Article Snippet: The PCR products obtained were inserted into the expression vector pET100/D-TOPO® (ThermoFisher Scientific, https://www.thermofisher.com ) (PtTPS16 and PtTPS21 ) or pASK-IBA7 (IBA-GmbH, Göttingen, Germany) (PnTPS4 ) and the cloned genes were fully sequenced. .. In vitro mutagenesis For site-directed mutagenesis, 100 ng pET100/D-TOPO® vector containing the N-terminal truncated ORF of PtTPS16 was used as template in a mutagenesis PCR (18 cycles, Phusion® High-Fidelity DNA Polymerase (ThermoFisher Scientific), according to manufacturer’s instructions. .. After PCR, the plasmid template DNA was digested with Dpn I and the reaction mixture was inserted and amplified in E. coli TOP10 (Invitrogen).

    Article Title: Effect of the enzyme and PCR conditions on the quality of high-throughput DNA sequencing results
    Article Snippet: Taq polymerase A range of 13 high fidelity, regular, economy and premium Taq polymerase enzymes were selected: Biotaq® (Bioline, London, UK), FastStart® High Fidelity PCR System (Roche, Mannheim, Germany), AmpliTaq Gold® (Applied Biosystems, Warrington, UK), HotStarTaq® DNA Polymerase (Qiagen, Hilden, Gernamy), Phusion® High Fidelity DNA Polymerase (Finnzymes, Espoo, Finland), Taq DNA Polymerase (Roche, Maylan, France), i-MaxTM II DNA Polymerase (iNtRON Biotechnology, Seongnam, Korea), KAPA HiFi™ (Kapa Biosystems, Boston, USA), OneTaq™ DNA Polymerase (New England Biolabs, Hitchin, UK), Vent® DNA Polymerase (New England Biolabs, Hitchin, UK), Deep Vent® DNA Polymerase (New England Biolabs, Hitchin, UK), Pwo® DNA Polymerase (Roche, Maylan, France) and Velocity DNA Polymerase (Bioline, London, UK) (abbreviated names in ). .. Taq polymerase A range of 13 high fidelity, regular, economy and premium Taq polymerase enzymes were selected: Biotaq® (Bioline, London, UK), FastStart® High Fidelity PCR System (Roche, Mannheim, Germany), AmpliTaq Gold® (Applied Biosystems, Warrington, UK), HotStarTaq® DNA Polymerase (Qiagen, Hilden, Gernamy), Phusion® High Fidelity DNA Polymerase (Finnzymes, Espoo, Finland), Taq DNA Polymerase (Roche, Maylan, France), i-MaxTM II DNA Polymerase (iNtRON Biotechnology, Seongnam, Korea), KAPA HiFi™ (Kapa Biosystems, Boston, USA), OneTaq ™ DNA Polymerase (New England Biolabs, Hitchin, UK), Vent® DNA Polymerase (New England Biolabs, Hitchin, UK), Deep Vent® DNA Polymerase (New England Biolabs, Hitchin, UK), Pwo® DNA Polymerase (Roche, Maylan, France) and Velocity DNA Polymerase (Bioline, London, UK) (abbreviated names in ). .. Assessment of accuracy for different enzymesLoci for Tests 1–3 were amplified in a two-step process following the universal tailed amplicon design proposed by Roche .

    Article Title: Selection of efficient Taq DNA polymerase to optimize T-DNA genotyping method for rapid detection of mutant Arabidopsis thaliana plants
    Article Snippet: .. The following DNA polymerases were tested: Phusion High-Fidelity DNA polymerase (ThermoFisher Scientific, USA, cat #F530S), Ex-Taq DNA polymerase (Clontech, USA, cat #RR001A), Taq DNA polymerase (SibEnzyme, Russia, cat #E331), Emerald Amp GT PCR Master Mix (Clontech, USA, cat #RR310A). .. 10 ng of genomic DNA and 10 μM of each primer were used in all PCR reactions; all other components of PCR reactions were added according to the manufacturer’s suggested protocol for each individual polymerase.

    Amplification:

    Article Title: Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes
    Article Snippet: From a single pool of adapter-ligated library, aliquots were amplified using standard Illumina PCR reagents or using various alternative polymerases under optimized PCR conditions. .. Standard Illumina PCR (50 μl) with Phusion polymerase (Thermo) contained 1× Phusion DNA polymerase master mix and 0.4 μM of each primer pair and was amplified with thermocycling conditions of 1 min at 98°C for the initial denaturation, followed by 12 cycles of [10 s at 98°C, 30 s at 65°C, 30 s at 72°C] and a final extension for 5 min at 72°C. .. PCR (50 μl) with Kapa HiFi (KAPA Biosystems, South Africa) contained 1× Kapa HiFi buffer (containing TMAC) or 1× Kapa buffer B, 0.3 mM of each dNTP, 0.4 μM of each primer pair, 1 unit of Kapa HiFi and was amplified with thermocycling conditions of 1 min at 98°C for the initial denaturation followed by 12 cycles of [10 s at 98°C, 1 min at 65°C] and a final extension for 5 min at 65°C.

    Article Title: Improvement of long segment ribosomal PCR amplification for molecular identification of Litylenchus crenatae mccannii associated with beech leaf disease
    Article Snippet: .. Phusion™ High-Fidelity DNA polymeraseEach PCR amplification with Phusion™ High-Fidelity DNA Polymerase (Thermo Fisher Scientific, Waltham, MA) was carried out in a 25 μl of mixture containing Phusion™ High-Fidelity DNA Polymerase (2 units/μl) 0.25 μl, 5× reaction buffer 5 μl, dNTP (2.5 mM each) 0.5 μl, Template DNA 2 μl, forward primer 18S-CL-F3 (10 μm) 1.25 μl, reverse primer 28S-CL-R (10 μm) 1.25 μl, DMSO 0.25 μl, and molecular biology grade water (Sigma-Aldrich, St Louis, MO) 14.5 μl. ..

    Article Title: Arabidopsis Calmodulin-binding Protein IQ67-Domain 1 Localizes to Microtubules and Interacts with Kinesin Light Chain-related Protein-1 *
    Article Snippet: To independently confirm interaction in the yeast two-hybrid system, the yeast strains Y187 and AH109 were transformed with the respective constructs, mated, and tested for growth on restrictive (−Trp-Leu-His-Ade) SD medium in the presence of 20 μg/ml of the chromogenic β-galactosidase substrate 5-bromo-4-chloro-indolyl-β- d -galactopyranoside (X-Gal). .. The coding sequences of IQD1, KLCR1, and CaM2 were amplified in combination with a high fidelity DNA polymerase and subsequently inserted into pENTR/D-TOPO plasmid via directional TOPO cloning (Invitrogen) to generate IQD1-, KLCR1-, and CaM2-pENTR/D-TOPO vectors. .. A derivative plasmid lacking the IQD1 stop codon, IQD1*-pENTR/D-TOPO, was generated via site-directed mutagenesis (Stratagene, La Jolla, CA) according to the manufacturer's protocol.

    In Vitro:

    Article Title: The occurrence and formation of monoterpenes in herbivore-damaged poplar roots
    Article Snippet: The PCR products obtained were inserted into the expression vector pET100/D-TOPO® (ThermoFisher Scientific, https://www.thermofisher.com ) (PtTPS16 and PtTPS21 ) or pASK-IBA7 (IBA-GmbH, Göttingen, Germany) (PnTPS4 ) and the cloned genes were fully sequenced. .. In vitro mutagenesis For site-directed mutagenesis, 100 ng pET100/D-TOPO® vector containing the N-terminal truncated ORF of PtTPS16 was used as template in a mutagenesis PCR (18 cycles, Phusion® High-Fidelity DNA Polymerase (ThermoFisher Scientific), according to manufacturer’s instructions. .. After PCR, the plasmid template DNA was digested with Dpn I and the reaction mixture was inserted and amplified in E. coli TOP10 (Invitrogen).

    Article Title: Efficient in situ barcode sequencing using padlock probe-based BaristaSeq
    Article Snippet: .. In vitro gap-filling assay In vitro gap-filling assays were performed in 1X Ampligase buffer (Epicentre) with 10 nM padlock probes (XC1149 and XC1151) and 10 nM cDNA template (XC1498), 20 μM dNTP, 0.012 U/μl Phusion High-Fidelity DNA Polymerase (Thermo Fisher Scientific) or Stoffel fragment (DNA Gdansk), additional 50 mM KCl, 20% formamide, and glycerol to a final concentration of 10%. .. The reaction was kept at 37°C for 30 min. We then terminated the reactions by adding 2× TBE Urea sample buffer (Thermo Fisher Scientific) and ran the samples on 15% Novex TBE–Urea gels (Thermo Fisher Scientific).

    Mutagenesis:

    Article Title: The occurrence and formation of monoterpenes in herbivore-damaged poplar roots
    Article Snippet: The PCR products obtained were inserted into the expression vector pET100/D-TOPO® (ThermoFisher Scientific, https://www.thermofisher.com ) (PtTPS16 and PtTPS21 ) or pASK-IBA7 (IBA-GmbH, Göttingen, Germany) (PnTPS4 ) and the cloned genes were fully sequenced. .. In vitro mutagenesis For site-directed mutagenesis, 100 ng pET100/D-TOPO® vector containing the N-terminal truncated ORF of PtTPS16 was used as template in a mutagenesis PCR (18 cycles, Phusion® High-Fidelity DNA Polymerase (ThermoFisher Scientific), according to manufacturer’s instructions. .. After PCR, the plasmid template DNA was digested with Dpn I and the reaction mixture was inserted and amplified in E. coli TOP10 (Invitrogen).

    Plasmid Preparation:

    Article Title: The occurrence and formation of monoterpenes in herbivore-damaged poplar roots
    Article Snippet: The PCR products obtained were inserted into the expression vector pET100/D-TOPO® (ThermoFisher Scientific, https://www.thermofisher.com ) (PtTPS16 and PtTPS21 ) or pASK-IBA7 (IBA-GmbH, Göttingen, Germany) (PnTPS4 ) and the cloned genes were fully sequenced. .. In vitro mutagenesis For site-directed mutagenesis, 100 ng pET100/D-TOPO® vector containing the N-terminal truncated ORF of PtTPS16 was used as template in a mutagenesis PCR (18 cycles, Phusion® High-Fidelity DNA Polymerase (ThermoFisher Scientific), according to manufacturer’s instructions. .. After PCR, the plasmid template DNA was digested with Dpn I and the reaction mixture was inserted and amplified in E. coli TOP10 (Invitrogen).

    Article Title: Arabidopsis Calmodulin-binding Protein IQ67-Domain 1 Localizes to Microtubules and Interacts with Kinesin Light Chain-related Protein-1 *
    Article Snippet: To independently confirm interaction in the yeast two-hybrid system, the yeast strains Y187 and AH109 were transformed with the respective constructs, mated, and tested for growth on restrictive (−Trp-Leu-His-Ade) SD medium in the presence of 20 μg/ml of the chromogenic β-galactosidase substrate 5-bromo-4-chloro-indolyl-β- d -galactopyranoside (X-Gal). .. The coding sequences of IQD1, KLCR1, and CaM2 were amplified in combination with a high fidelity DNA polymerase and subsequently inserted into pENTR/D-TOPO plasmid via directional TOPO cloning (Invitrogen) to generate IQD1-, KLCR1-, and CaM2-pENTR/D-TOPO vectors. .. A derivative plasmid lacking the IQD1 stop codon, IQD1*-pENTR/D-TOPO, was generated via site-directed mutagenesis (Stratagene, La Jolla, CA) according to the manufacturer's protocol.

    Concentration Assay:

    Article Title: Efficient in situ barcode sequencing using padlock probe-based BaristaSeq
    Article Snippet: .. In vitro gap-filling assay In vitro gap-filling assays were performed in 1X Ampligase buffer (Epicentre) with 10 nM padlock probes (XC1149 and XC1151) and 10 nM cDNA template (XC1498), 20 μM dNTP, 0.012 U/μl Phusion High-Fidelity DNA Polymerase (Thermo Fisher Scientific) or Stoffel fragment (DNA Gdansk), additional 50 mM KCl, 20% formamide, and glycerol to a final concentration of 10%. .. The reaction was kept at 37°C for 30 min. We then terminated the reactions by adding 2× TBE Urea sample buffer (Thermo Fisher Scientific) and ran the samples on 15% Novex TBE–Urea gels (Thermo Fisher Scientific).

    Clone Assay:

    Article Title: Arabidopsis Calmodulin-binding Protein IQ67-Domain 1 Localizes to Microtubules and Interacts with Kinesin Light Chain-related Protein-1 *
    Article Snippet: To independently confirm interaction in the yeast two-hybrid system, the yeast strains Y187 and AH109 were transformed with the respective constructs, mated, and tested for growth on restrictive (−Trp-Leu-His-Ade) SD medium in the presence of 20 μg/ml of the chromogenic β-galactosidase substrate 5-bromo-4-chloro-indolyl-β- d -galactopyranoside (X-Gal). .. The coding sequences of IQD1, KLCR1, and CaM2 were amplified in combination with a high fidelity DNA polymerase and subsequently inserted into pENTR/D-TOPO plasmid via directional TOPO cloning (Invitrogen) to generate IQD1-, KLCR1-, and CaM2-pENTR/D-TOPO vectors. .. A derivative plasmid lacking the IQD1 stop codon, IQD1*-pENTR/D-TOPO, was generated via site-directed mutagenesis (Stratagene, La Jolla, CA) according to the manufacturer's protocol.

    other:

    Article Title: Improvement of long segment ribosomal PCR amplification for molecular identification of Litylenchus crenatae mccannii associated with beech leaf disease
    Article Snippet: Herculase® II Fusion DNA polymerase and Phusion™ High-Fidelity DNA Polymerase were tested. shows both could not produce any 3.5 kb target bands except for the smear band by the Herculase® II Fusion DNA polymerase.

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 97
    Thermo Fisher pcr amplification
    Genotype analysis of the generated PfΔ slarp and PfΔ b9 Δ slarp parasites . ( A ) Long range <t>PCR</t> analysis of genomic <t>DNA</t> from WT, Pf Δ slarp and Pf Δ b9 Δ slarp asexual parasites confirms the slarp gene deletion and consecutive gene deletions of both slarp and b9 respectively and subsequent removal of the hdhfr::gfp resistance marker. The PCR products are generated using primers P1,P2 for slarp and P3,P4 for b9 (see A and B respectively; for primer sequences see primer table in Supplementary file 2B ) and PCR products are also digested with restriction enzymes x ( Xma I) and kx ( Kpn I/ Xcm I) respectively for confirmation (i.e. slarp LR-PCR product sizes: WT, 12 kb, is undigested; Δ slarp-a , 5.4 kb is digested into 1.3 kb and 4.0 kb fragments, Δ slarp-b , 2.4 kb is digested into 1.3 kb and 1.1 kb fragments. b9 LR-PCR product sizes: WT, 5.5 kb, is digested into 756 bp, 793 bp, and 4.0 kb fragments; Δ b9-b , 2.6 kb is digested into 756 bp, 793 bp, and 1.1 kb fragments). ( B ) Southern analysis of restricted genomic DNA from WT, PfΔ slarp- a, PfΔ slarp- b, PfΔ b9 Δ slarp -F7, and PfΔ b9 Δ slarp -G9 asexual parasites. DNA was digested with restriction enzyme (E: Taq I) and probed with the 5′ slarp targeting region (P: 5′ slarp -T; see A ) on the left side of the slarp Southern or probed with the 3′ slarp targeting region (P: 3′ slarp -T; see A ) on the right side of the slarp panel. For analysis of the b9 , integration DNA was digested with restriction enzymes (E: Rca I) and probed with the 5′ b9 targeting region (P: 5′ b9 -T; see A ) on the right panel. The expected fragment sizes are indicated in panel ( A ). ( C ) RT-PCR analysis showing the absence of b9 and slarp transcripts in P. falciparum PfΔ slarp- a, PfΔ slarp- b, PfΔ b9 Δ slarp -F7, and PfΔ b9 Δ slarp -G9 mutant sporozoites. PCR amplification using purified sporozoite RNA was performed either in the presence or absence of reverse transcriptase (RT+ or RT−, respectively) and generated the expected 506 bp and 580 bp fragments for slarp and b9 respectively, the positive control was performed by PCR of 18S rRNA using primers 18Sf/18Sr (for primer sequences see Supplementary file 2B ) and generated the expected 130 bp fragment. DOI: http://dx.doi.org/10.7554/eLife.03582.009
    Pcr Amplification, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/pcr amplification/product/Thermo Fisher
    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    pcr amplification - by Bioz Stars, 2021-03
    97/100 stars
      Buy from Supplier

    97
    Thermo Fisher phusion high fidelity dna polymeraseeach pcr amplification
    <t>PCR</t> performance of Herculase® II Fusion <t>DNA</t> polymerase and <t>Phusion™</t> High-Fidelity DNA Polymerase. M: DNA markers; 1 and 5: 104K37; 2 and 6: 104K38; 3 and 7: 104K39; 4 and 8: 104K40. 1, 2, 3 and 4: Herculase® II Fusion DNA polymerase; 5, 6, 7 and 8: Phusion™ High Fidelity PCR System; NC: negative control, respectively.
    Phusion High Fidelity Dna Polymeraseeach Pcr Amplification, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 97/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phusion high fidelity dna polymeraseeach pcr amplification/product/Thermo Fisher
    Average 97 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    phusion high fidelity dna polymeraseeach pcr amplification - by Bioz Stars, 2021-03
    97/100 stars
      Buy from Supplier

    Image Search Results


    Genotype analysis of the generated PfΔ slarp and PfΔ b9 Δ slarp parasites . ( A ) Long range PCR analysis of genomic DNA from WT, Pf Δ slarp and Pf Δ b9 Δ slarp asexual parasites confirms the slarp gene deletion and consecutive gene deletions of both slarp and b9 respectively and subsequent removal of the hdhfr::gfp resistance marker. The PCR products are generated using primers P1,P2 for slarp and P3,P4 for b9 (see A and B respectively; for primer sequences see primer table in Supplementary file 2B ) and PCR products are also digested with restriction enzymes x ( Xma I) and kx ( Kpn I/ Xcm I) respectively for confirmation (i.e. slarp LR-PCR product sizes: WT, 12 kb, is undigested; Δ slarp-a , 5.4 kb is digested into 1.3 kb and 4.0 kb fragments, Δ slarp-b , 2.4 kb is digested into 1.3 kb and 1.1 kb fragments. b9 LR-PCR product sizes: WT, 5.5 kb, is digested into 756 bp, 793 bp, and 4.0 kb fragments; Δ b9-b , 2.6 kb is digested into 756 bp, 793 bp, and 1.1 kb fragments). ( B ) Southern analysis of restricted genomic DNA from WT, PfΔ slarp- a, PfΔ slarp- b, PfΔ b9 Δ slarp -F7, and PfΔ b9 Δ slarp -G9 asexual parasites. DNA was digested with restriction enzyme (E: Taq I) and probed with the 5′ slarp targeting region (P: 5′ slarp -T; see A ) on the left side of the slarp Southern or probed with the 3′ slarp targeting region (P: 3′ slarp -T; see A ) on the right side of the slarp panel. For analysis of the b9 , integration DNA was digested with restriction enzymes (E: Rca I) and probed with the 5′ b9 targeting region (P: 5′ b9 -T; see A ) on the right panel. The expected fragment sizes are indicated in panel ( A ). ( C ) RT-PCR analysis showing the absence of b9 and slarp transcripts in P. falciparum PfΔ slarp- a, PfΔ slarp- b, PfΔ b9 Δ slarp -F7, and PfΔ b9 Δ slarp -G9 mutant sporozoites. PCR amplification using purified sporozoite RNA was performed either in the presence or absence of reverse transcriptase (RT+ or RT−, respectively) and generated the expected 506 bp and 580 bp fragments for slarp and b9 respectively, the positive control was performed by PCR of 18S rRNA using primers 18Sf/18Sr (for primer sequences see Supplementary file 2B ) and generated the expected 130 bp fragment. DOI: http://dx.doi.org/10.7554/eLife.03582.009

    Journal: eLife

    Article Title: A genetically attenuated malaria vaccine candidate based on P. falciparum b9/slarp gene-deficient sporozoites

    doi: 10.7554/eLife.03582

    Figure Lengend Snippet: Genotype analysis of the generated PfΔ slarp and PfΔ b9 Δ slarp parasites . ( A ) Long range PCR analysis of genomic DNA from WT, Pf Δ slarp and Pf Δ b9 Δ slarp asexual parasites confirms the slarp gene deletion and consecutive gene deletions of both slarp and b9 respectively and subsequent removal of the hdhfr::gfp resistance marker. The PCR products are generated using primers P1,P2 for slarp and P3,P4 for b9 (see A and B respectively; for primer sequences see primer table in Supplementary file 2B ) and PCR products are also digested with restriction enzymes x ( Xma I) and kx ( Kpn I/ Xcm I) respectively for confirmation (i.e. slarp LR-PCR product sizes: WT, 12 kb, is undigested; Δ slarp-a , 5.4 kb is digested into 1.3 kb and 4.0 kb fragments, Δ slarp-b , 2.4 kb is digested into 1.3 kb and 1.1 kb fragments. b9 LR-PCR product sizes: WT, 5.5 kb, is digested into 756 bp, 793 bp, and 4.0 kb fragments; Δ b9-b , 2.6 kb is digested into 756 bp, 793 bp, and 1.1 kb fragments). ( B ) Southern analysis of restricted genomic DNA from WT, PfΔ slarp- a, PfΔ slarp- b, PfΔ b9 Δ slarp -F7, and PfΔ b9 Δ slarp -G9 asexual parasites. DNA was digested with restriction enzyme (E: Taq I) and probed with the 5′ slarp targeting region (P: 5′ slarp -T; see A ) on the left side of the slarp Southern or probed with the 3′ slarp targeting region (P: 3′ slarp -T; see A ) on the right side of the slarp panel. For analysis of the b9 , integration DNA was digested with restriction enzymes (E: Rca I) and probed with the 5′ b9 targeting region (P: 5′ b9 -T; see A ) on the right panel. The expected fragment sizes are indicated in panel ( A ). ( C ) RT-PCR analysis showing the absence of b9 and slarp transcripts in P. falciparum PfΔ slarp- a, PfΔ slarp- b, PfΔ b9 Δ slarp -F7, and PfΔ b9 Δ slarp -G9 mutant sporozoites. PCR amplification using purified sporozoite RNA was performed either in the presence or absence of reverse transcriptase (RT+ or RT−, respectively) and generated the expected 506 bp and 580 bp fragments for slarp and b9 respectively, the positive control was performed by PCR of 18S rRNA using primers 18Sf/18Sr (for primer sequences see Supplementary file 2B ) and generated the expected 130 bp fragment. DOI: http://dx.doi.org/10.7554/eLife.03582.009

    Article Snippet: All DNA fragments were amplified by PCR amplification (Phusion, Finnzymes) from genomic P. falciparum DNA (NF54 strain) and all PCR fragments were sequenced after TOPO TA (Invitrogen, Leek, The Netherlands) sub-cloning.

    Techniques: Generated, Polymerase Chain Reaction, Marker, Reverse Transcription Polymerase Chain Reaction, Mutagenesis, Amplification, Purification, Positive Control

    Generation and genotype analyses of P. berghei mutant PbΔ slarp- a . ( A ) Generation of mutant PbΔ slarp -a. For PbΔ slarp -a, the DNA-construct pL1740 was generated containing the positive/negative selectable marker cassette hdhfr / yfcy . This construct was subsequently used to generate the mutant PbΔ slarp -a (1839cl3) in the Pb GFP-Luc con reference line. See Supplementary file 2A for the sequence of the primers. ( B ) Diagnostic PCR and Southern analysis of Pulse Field Gel (PFG)-separated chromosomes of mutant Δ slarp -a confirming correct disruption of the slarp -locus. See Supplementary file 2A for the sequence of the primers used for the selectable marker gene (SM); 5′-integration event (5′); 3′-integration event (3′); and the slarp ORF. Mutant PbΔ slarp -a has been generated in the reference P. berghei ANKA line Pb GFP-Luc con which has a gfp-luciferase gene integrated into the silent 230p locus (PBANKA_030600) on chromosome 3. For Southern analysis, PFG-separated chromosomes were hybridized using a 3′UTR pbdhfr probe that recognizes the construct integrated into P. berghei slarp locus on chromosome 9, the endogenous locus of dhfr/ts on chromosome 7, and the gfp-luciferase gene integrated into chromosome 3. In addition, the chromosomes were hybridized with the hdhfr probe recognizing the integrated construct into the slarp locus on chromosome 9. ( C ) Real time in vivo imaging of Δslarp luciferase-expressing liver-stage parasites in C57BL/6 mice at 24, 35, and 45 hr post-infection. C57BL/6 mice were IV injected with either 5 × 10 4 Pb -GFPLuc con sporozoites (n = 5), resulting in a full liver infection (upper panel: representative image of WT infected mice), or with 5 × 10 5 Pb Δslarp-a sporozoites (n = 5) (lower panel: representative image of Pb Δslarp-luc infected mice). DOI: http://dx.doi.org/10.7554/eLife.03582.006

    Journal: eLife

    Article Title: A genetically attenuated malaria vaccine candidate based on P. falciparum b9/slarp gene-deficient sporozoites

    doi: 10.7554/eLife.03582

    Figure Lengend Snippet: Generation and genotype analyses of P. berghei mutant PbΔ slarp- a . ( A ) Generation of mutant PbΔ slarp -a. For PbΔ slarp -a, the DNA-construct pL1740 was generated containing the positive/negative selectable marker cassette hdhfr / yfcy . This construct was subsequently used to generate the mutant PbΔ slarp -a (1839cl3) in the Pb GFP-Luc con reference line. See Supplementary file 2A for the sequence of the primers. ( B ) Diagnostic PCR and Southern analysis of Pulse Field Gel (PFG)-separated chromosomes of mutant Δ slarp -a confirming correct disruption of the slarp -locus. See Supplementary file 2A for the sequence of the primers used for the selectable marker gene (SM); 5′-integration event (5′); 3′-integration event (3′); and the slarp ORF. Mutant PbΔ slarp -a has been generated in the reference P. berghei ANKA line Pb GFP-Luc con which has a gfp-luciferase gene integrated into the silent 230p locus (PBANKA_030600) on chromosome 3. For Southern analysis, PFG-separated chromosomes were hybridized using a 3′UTR pbdhfr probe that recognizes the construct integrated into P. berghei slarp locus on chromosome 9, the endogenous locus of dhfr/ts on chromosome 7, and the gfp-luciferase gene integrated into chromosome 3. In addition, the chromosomes were hybridized with the hdhfr probe recognizing the integrated construct into the slarp locus on chromosome 9. ( C ) Real time in vivo imaging of Δslarp luciferase-expressing liver-stage parasites in C57BL/6 mice at 24, 35, and 45 hr post-infection. C57BL/6 mice were IV injected with either 5 × 10 4 Pb -GFPLuc con sporozoites (n = 5), resulting in a full liver infection (upper panel: representative image of WT infected mice), or with 5 × 10 5 Pb Δslarp-a sporozoites (n = 5) (lower panel: representative image of Pb Δslarp-luc infected mice). DOI: http://dx.doi.org/10.7554/eLife.03582.006

    Article Snippet: All DNA fragments were amplified by PCR amplification (Phusion, Finnzymes) from genomic P. falciparum DNA (NF54 strain) and all PCR fragments were sequenced after TOPO TA (Invitrogen, Leek, The Netherlands) sub-cloning.

    Techniques: Mutagenesis, Construct, Generated, Marker, Sequencing, Diagnostic Assay, Polymerase Chain Reaction, Luciferase, In Vivo Imaging, Expressing, Mouse Assay, Infection, Injection

    PCR performance of Herculase® II Fusion DNA polymerase and Phusion™ High-Fidelity DNA Polymerase. M: DNA markers; 1 and 5: 104K37; 2 and 6: 104K38; 3 and 7: 104K39; 4 and 8: 104K40. 1, 2, 3 and 4: Herculase® II Fusion DNA polymerase; 5, 6, 7 and 8: Phusion™ High Fidelity PCR System; NC: negative control, respectively.

    Journal: Journal of Nematology

    Article Title: Improvement of long segment ribosomal PCR amplification for molecular identification of Litylenchus crenatae mccannii associated with beech leaf disease

    doi: 10.21307/jofnem-2020-016

    Figure Lengend Snippet: PCR performance of Herculase® II Fusion DNA polymerase and Phusion™ High-Fidelity DNA Polymerase. M: DNA markers; 1 and 5: 104K37; 2 and 6: 104K38; 3 and 7: 104K39; 4 and 8: 104K40. 1, 2, 3 and 4: Herculase® II Fusion DNA polymerase; 5, 6, 7 and 8: Phusion™ High Fidelity PCR System; NC: negative control, respectively.

    Article Snippet: Phusion™ High-Fidelity DNA polymeraseEach PCR amplification with Phusion™ High-Fidelity DNA Polymerase (Thermo Fisher Scientific, Waltham, MA) was carried out in a 25 μl of mixture containing Phusion™ High-Fidelity DNA Polymerase (2 units/μl) 0.25 μl, 5× reaction buffer 5 μl, dNTP (2.5 mM each) 0.5 μl, Template DNA 2 μl, forward primer 18S-CL-F3 (10 μm) 1.25 μl, reverse primer 28S-CL-R (10 μm) 1.25 μl, DMSO 0.25 μl, and molecular biology grade water (Sigma-Aldrich, St Louis, MO) 14.5 μl.

    Techniques: Polymerase Chain Reaction, Negative Control

    Genotyping of Arabidopsis thaliana plants from SALK_100012 line with (a) Phusion High-Fidelity DNA polymerase; (b) Ex-Taq DNA polymerase; (c) Taq DNA polymerase; (d) Emerald Amp GT PCR Master Mix. WT - DNA from wild-type Arabidopsis plant (positive control for wild-type PCR band); 1–8 - individual plants from SALK_100012 line. Molecular weight DNA standards are shown on each side. Loading order for each DNA sample: PCR reaction for wild-type allele, PCR reaction for T-DNA mutant allele.

    Journal: BioNanoScience

    Article Title: Selection of efficient Taq DNA polymerase to optimize T-DNA genotyping method for rapid detection of mutant Arabidopsis thaliana plants

    doi: 10.1007/s12668-016-0253-6

    Figure Lengend Snippet: Genotyping of Arabidopsis thaliana plants from SALK_100012 line with (a) Phusion High-Fidelity DNA polymerase; (b) Ex-Taq DNA polymerase; (c) Taq DNA polymerase; (d) Emerald Amp GT PCR Master Mix. WT - DNA from wild-type Arabidopsis plant (positive control for wild-type PCR band); 1–8 - individual plants from SALK_100012 line. Molecular weight DNA standards are shown on each side. Loading order for each DNA sample: PCR reaction for wild-type allele, PCR reaction for T-DNA mutant allele.

    Article Snippet: The following DNA polymerases were tested: Phusion High-Fidelity DNA polymerase (ThermoFisher Scientific, USA, cat #F530S), Ex-Taq DNA polymerase (Clontech, USA, cat #RR001A), Taq DNA polymerase (SibEnzyme, Russia, cat #E331), Emerald Amp GT PCR Master Mix (Clontech, USA, cat #RR310A).

    Techniques: Polymerase Chain Reaction, Positive Control, Molecular Weight, Mutagenesis

    Proportion of correct reads for the three genetic systems (simple: a single allele per individual, squares ; medium: two alleles, circles ; and complex: multiple alleles, triangles ) using standard PCR conditions ( open ) and modified PCR conditions to reduce chimera formation ( gray ). The size of the shape is indicative of the number of reads (see legend). All enzymes yielded at least 50% correct reads in the simplest system, mitochondrial DNA (Test 1; open squares). Some enzymes only worked for a given set of conditions (cycling conditions/genetic system). A group of enzymes consisting of Phusion, Gold and FastStart yielded a high proportion of correct reads cosistently accross all conditions. Others, such as Roche Taq, HotStar and Biotaq, yielded a low percent of correct reads for the more complex systems (MHC class I and MHC class II). Abbreviations as defined in Table 1 .

    Journal: Scientific Reports

    Article Title: Effect of the enzyme and PCR conditions on the quality of high-throughput DNA sequencing results

    doi: 10.1038/srep08056

    Figure Lengend Snippet: Proportion of correct reads for the three genetic systems (simple: a single allele per individual, squares ; medium: two alleles, circles ; and complex: multiple alleles, triangles ) using standard PCR conditions ( open ) and modified PCR conditions to reduce chimera formation ( gray ). The size of the shape is indicative of the number of reads (see legend). All enzymes yielded at least 50% correct reads in the simplest system, mitochondrial DNA (Test 1; open squares). Some enzymes only worked for a given set of conditions (cycling conditions/genetic system). A group of enzymes consisting of Phusion, Gold and FastStart yielded a high proportion of correct reads cosistently accross all conditions. Others, such as Roche Taq, HotStar and Biotaq, yielded a low percent of correct reads for the more complex systems (MHC class I and MHC class II). Abbreviations as defined in Table 1 .

    Article Snippet: Taq polymerase A range of 13 high fidelity, regular, economy and premium Taq polymerase enzymes were selected: Biotaq® (Bioline, London, UK), FastStart® High Fidelity PCR System (Roche, Mannheim, Germany), AmpliTaq Gold® (Applied Biosystems, Warrington, UK), HotStarTaq® DNA Polymerase (Qiagen, Hilden, Gernamy), Phusion® High Fidelity DNA Polymerase (Finnzymes, Espoo, Finland), Taq DNA Polymerase (Roche, Maylan, France), i-MaxTM II DNA Polymerase (iNtRON Biotechnology, Seongnam, Korea), KAPA HiFi™ (Kapa Biosystems, Boston, USA), OneTaq ™ DNA Polymerase (New England Biolabs, Hitchin, UK), Vent® DNA Polymerase (New England Biolabs, Hitchin, UK), Deep Vent® DNA Polymerase (New England Biolabs, Hitchin, UK), Pwo® DNA Polymerase (Roche, Maylan, France) and Velocity DNA Polymerase (Bioline, London, UK) (abbreviated names in ).

    Techniques: Polymerase Chain Reaction, Modification