phusion polymerase chain reaction mix  (New England Biolabs)


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  • 99
    Name:
    Poly U Polymerase
    Description:
    Poly U Polymerase 60 units
    Catalog Number:
    m0337s
    Price:
    90
    Size:
    60 units
    Category:
    RNA Polymerases
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    Structured Review

    New England Biolabs phusion polymerase chain reaction mix
    Poly U Polymerase
    Poly U Polymerase 60 units
    https://www.bioz.com/result/phusion polymerase chain reaction mix/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    phusion polymerase chain reaction mix - by Bioz Stars, 2020-08
    99/100 stars

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    Related Articles

    Amplification:

    Article Title: Circularization pathway of a bacterial group II intron
    Article Snippet: .. For Ll.LtrB-ΔA a second amplification of the 3′ end was performed where a polyU instead of a polyA tail was added using 2U of Poly(U) Polymerase (New England Biolabs) (10 min at 37°C). ..

    Article Title: Serotype-specific interactions among functional domains of dengue virus 2 nonstructural proteins (NS) 5 and NS3 are crucial for viral RNA replication
    Article Snippet: .. The synthesized viral cDNA from collected supernatants was amplified by PCR using NEBNext High Fidelity 2× polymerase (New England Biolabs) and the viral sequence-specific primers (Ref. and ) to make overlapping fragments (each ∼800 bp) that spanned the entire genome. .. PCR products were purified by agarose gel (Zymo Research), and the nucleotide sequence of each fragment was determined by GENEWIZ Inc.

    Synthesized:

    Article Title: Serotype-specific interactions among functional domains of dengue virus 2 nonstructural proteins (NS) 5 and NS3 are crucial for viral RNA replication
    Article Snippet: .. The synthesized viral cDNA from collected supernatants was amplified by PCR using NEBNext High Fidelity 2× polymerase (New England Biolabs) and the viral sequence-specific primers (Ref. and ) to make overlapping fragments (each ∼800 bp) that spanned the entire genome. .. PCR products were purified by agarose gel (Zymo Research), and the nucleotide sequence of each fragment was determined by GENEWIZ Inc.

    Mutagenesis:

    Article Title: Sequences in the U3 region of Human Immunodeficiency Virus 1 improve efficiency of minus strand transfer in infected cells
    Article Snippet: .. For mutant M9-m, two PCR products were produced using pairs of oligomers 1/3 and 4/2 and VENT polymerase (NewEngland Biolabs). ..

    Quantitation Assay:

    Article Title: Decreased miR-155-5p, miR-15a, and miR-186 Expression in Gastric Cancer Is Associated with Advanced Tumor Grade and Metastasis
    Article Snippet: .. MiRNA quantitation Briefly, a poly-A tail was added to total RNAs (500 ng) using Poly-A polymerase (New England Biolabs, UK) at 37 °C for 30 min according to manufacturer’s protocol. .. For cDNA synthesis, we used PrimeScript™ 1st strand cDNA Synthesis Kit (TaKaRa, Japan) and an RT adaptor primer ( ).

    Labeling:

    Article Title: A High-Throughput Small-Molecule Ligand Screen Targeted to Agonists and Antagonists of the G-Protein-Coupled Receptor GPR54
    Article Snippet: .. Total RNA was separated on a denaturing MOPS gel, blotted onto a nylon membrane (Schleicher & Schuell, Keene, NH), and hybridized with a GPR54 cRNA probe labeled with [α-32 P]UTP (PerkinElmer, Waltham, MA) using RNA polymerase (New England Biolabs). ..

    Produced:

    Article Title: Sequences in the U3 region of Human Immunodeficiency Virus 1 improve efficiency of minus strand transfer in infected cells
    Article Snippet: .. For mutant M9-m, two PCR products were produced using pairs of oligomers 1/3 and 4/2 and VENT polymerase (NewEngland Biolabs). ..

    Polymerase Chain Reaction:

    Article Title: Serotype-specific interactions among functional domains of dengue virus 2 nonstructural proteins (NS) 5 and NS3 are crucial for viral RNA replication
    Article Snippet: .. The synthesized viral cDNA from collected supernatants was amplified by PCR using NEBNext High Fidelity 2× polymerase (New England Biolabs) and the viral sequence-specific primers (Ref. and ) to make overlapping fragments (each ∼800 bp) that spanned the entire genome. .. PCR products were purified by agarose gel (Zymo Research), and the nucleotide sequence of each fragment was determined by GENEWIZ Inc.

    Article Title: Sequences in the U3 region of Human Immunodeficiency Virus 1 improve efficiency of minus strand transfer in infected cells
    Article Snippet: .. For mutant M9-m, two PCR products were produced using pairs of oligomers 1/3 and 4/2 and VENT polymerase (NewEngland Biolabs). ..

    Incubation:

    Article Title: Hallmarks of Hepatitis C Virus in Equine Hepacivirus
    Article Snippet: .. The poly(U) tail was added to the 3′ end of the RNA preparation using Escherichia coli poly(U) polymerase (New England BioLabs, Ipswich, MA) and was incubated for 45 min at 37°C. .. The resulting preparation was reverse transcribed by the SuperScript First-Strand Synthesis system (Life Technologies) using an oligo(dA) adapter primer (5′-TTGCGAGCACAGAATTAATACGACTCACAAAAAAAAAAAAVN-3′).

    Sequencing:

    Article Title: Serotype-specific interactions among functional domains of dengue virus 2 nonstructural proteins (NS) 5 and NS3 are crucial for viral RNA replication
    Article Snippet: .. The synthesized viral cDNA from collected supernatants was amplified by PCR using NEBNext High Fidelity 2× polymerase (New England Biolabs) and the viral sequence-specific primers (Ref. and ) to make overlapping fragments (each ∼800 bp) that spanned the entire genome. .. PCR products were purified by agarose gel (Zymo Research), and the nucleotide sequence of each fragment was determined by GENEWIZ Inc.

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  • 99
    New England Biolabs phusion high fidelity pcr master mix
    Agarose gel electrophoresis analysis of <t>PCR</t> fragments multiplied by <t>Phusion</t> High-Fidelity PCR Master Mix with HF Buffer and Phusion High-Fidelity PCR Master Mix with GC Buffer. Analysed PCRs are labelled as the mutated residue and the letter indicating whether the fragment is multiplied by mutation-specific forward (F) or reverse (R) primer. Expected PCR fragments are between 3000 and 4000 bp long. While using the PCR master mix with GC buffer gave expected fragments in all shown cases, using the Phusion High-Fidelity polymerase with HF buffer failed to multiply four fragments.
    Phusion High Fidelity Pcr Master Mix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 739 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phusion high fidelity pcr master mix/product/New England Biolabs
    Average 99 stars, based on 739 article reviews
    Price from $9.99 to $1999.99
    phusion high fidelity pcr master mix - by Bioz Stars, 2020-08
    99/100 stars
      Buy from Supplier

    88
    New England Biolabs phusion flash master mix
    Preparation of paired-end sequencing libraries from Sordaria macrospora. ( a ) and sheared by sonication with a Branson 450 Sonifier with microtip (duty cycle 80%, output 1.2; five cycles of 10 s pulses, interrupted by 30 s rest on ice). Sheared DNA was concentrated (Qiagen PCR purification kit) and separated on a 1.2% agarose gel. Gel slices of ∼300 and ∼500 bp fragments were isolated and purified (Qiagen Gel extraction kit, see Subheading 3.4, step 5). ( b ) Paired-end libraries were constructed as described in the methods from the 300- and 500-bp fractions and amplified with 12 cycles of PCR, yielding barely visible bands. Note presence of adapters and PCR primers below the 100 bp marker. ( c ) Test for library complexity. One simple test to show that libraries contain predominantly genomic DNA and are not enriched for adapter dimers or other spurious overamplified bands is to digest the DyNAzyme-amplified libraries with Dpn II. This cleaves most of the adapter off the inserts. If genomic DNA has been cloned it will result in a smear (similar to genomic DNA digested for Southern blots). If only low complexity samples have been cloned in the library, sharp banding is observed instead of the smear and the library is unsuitable for further processing. ( d ) Libraries were amplified with 18 cycles of PCR with <t>Phusion</t> Flash High-Fidelity polymerase and purified (Qiagen PCR purification kit; see three 300-bp library samples). We typically pool three independent 25 μmL PCR reactions before purification and run 5 μL of 35 μL to show that only expected bands are obtained. Note the absence of the adapters or PCR primers and primer dimers (compare to ( b )).
    Phusion Flash Master Mix, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 88/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phusion flash master mix/product/New England Biolabs
    Average 88 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    phusion flash master mix - by Bioz Stars, 2020-08
    88/100 stars
      Buy from Supplier

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    Agarose gel electrophoresis analysis of PCR fragments multiplied by Phusion High-Fidelity PCR Master Mix with HF Buffer and Phusion High-Fidelity PCR Master Mix with GC Buffer. Analysed PCRs are labelled as the mutated residue and the letter indicating whether the fragment is multiplied by mutation-specific forward (F) or reverse (R) primer. Expected PCR fragments are between 3000 and 4000 bp long. While using the PCR master mix with GC buffer gave expected fragments in all shown cases, using the Phusion High-Fidelity polymerase with HF buffer failed to multiply four fragments.

    Journal: Scientific Reports

    Article Title: High-throughput mutagenesis using a two-fragment PCR approach

    doi: 10.1038/s41598-017-07010-4

    Figure Lengend Snippet: Agarose gel electrophoresis analysis of PCR fragments multiplied by Phusion High-Fidelity PCR Master Mix with HF Buffer and Phusion High-Fidelity PCR Master Mix with GC Buffer. Analysed PCRs are labelled as the mutated residue and the letter indicating whether the fragment is multiplied by mutation-specific forward (F) or reverse (R) primer. Expected PCR fragments are between 3000 and 4000 bp long. While using the PCR master mix with GC buffer gave expected fragments in all shown cases, using the Phusion High-Fidelity polymerase with HF buffer failed to multiply four fragments.

    Article Snippet: PCR set-up and high-throughput mutagenesis PCR conditions were first tested for a random set of 30 CB2 mutants using Phusion High-Fidelity PCR Master Mix with HF Buffer, Phusion High-Fidelity PCR Master Mix with GC Buffer (New England Biolabs, NEB) and KOD Hot Start Master Mix (Merck Millipore).

    Techniques: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Mutagenesis

    '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: Standard reactions contained 1× Phusion High-Fidelity PCR master mix with HF buffer (NEB).

    Techniques: Genome Wide, Amplification, Polymerase Chain Reaction

    Effect of temperature ramp rates . The standard PCR protocol with Phusion HF DNA polymerase and short initial (30 s) and in-cycle (10 s) denaturation times was performed on three different thermocyclers at their respective default temperature ramp settings. Heating and cooling rates were 6°C/s and 4.5°C/s on thermocycler 1 (bright red line), 4°C/s and 3°C/s on thermocycler 2 (purple line) and 2.2°C/s and 2.2°C/s on thermocycler 3 (dark red line).

    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: Effect of temperature ramp rates . The standard PCR protocol with Phusion HF DNA polymerase and short initial (30 s) and in-cycle (10 s) denaturation times was performed on three different thermocyclers at their respective default temperature ramp settings. Heating and cooling rates were 6°C/s and 4.5°C/s on thermocycler 1 (bright red line), 4°C/s and 3°C/s on thermocycler 2 (purple line) and 2.2°C/s and 2.2°C/s on thermocycler 3 (dark red line).

    Article Snippet: Standard reactions contained 1× Phusion High-Fidelity PCR master mix with HF buffer (NEB).

    Techniques: Polymerase Chain Reaction

    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: Standard reactions contained 1× Phusion High-Fidelity PCR master mix with HF buffer (NEB).

    Techniques: Polymerase Chain Reaction

    Preparation of paired-end sequencing libraries from Sordaria macrospora. ( a ) and sheared by sonication with a Branson 450 Sonifier with microtip (duty cycle 80%, output 1.2; five cycles of 10 s pulses, interrupted by 30 s rest on ice). Sheared DNA was concentrated (Qiagen PCR purification kit) and separated on a 1.2% agarose gel. Gel slices of ∼300 and ∼500 bp fragments were isolated and purified (Qiagen Gel extraction kit, see Subheading 3.4, step 5). ( b ) Paired-end libraries were constructed as described in the methods from the 300- and 500-bp fractions and amplified with 12 cycles of PCR, yielding barely visible bands. Note presence of adapters and PCR primers below the 100 bp marker. ( c ) Test for library complexity. One simple test to show that libraries contain predominantly genomic DNA and are not enriched for adapter dimers or other spurious overamplified bands is to digest the DyNAzyme-amplified libraries with Dpn II. This cleaves most of the adapter off the inserts. If genomic DNA has been cloned it will result in a smear (similar to genomic DNA digested for Southern blots). If only low complexity samples have been cloned in the library, sharp banding is observed instead of the smear and the library is unsuitable for further processing. ( d ) Libraries were amplified with 18 cycles of PCR with Phusion Flash High-Fidelity polymerase and purified (Qiagen PCR purification kit; see three 300-bp library samples). We typically pool three independent 25 μmL PCR reactions before purification and run 5 μL of 35 μL to show that only expected bands are obtained. Note the absence of the adapters or PCR primers and primer dimers (compare to ( b )).

    Journal: Methods in molecular biology (Clifton, N.J.)

    Article Title: Library Preparation and Data Analysis Packages for Rapid Genome Sequencing

    doi: 10.1007/978-1-62703-122-6_1

    Figure Lengend Snippet: Preparation of paired-end sequencing libraries from Sordaria macrospora. ( a ) and sheared by sonication with a Branson 450 Sonifier with microtip (duty cycle 80%, output 1.2; five cycles of 10 s pulses, interrupted by 30 s rest on ice). Sheared DNA was concentrated (Qiagen PCR purification kit) and separated on a 1.2% agarose gel. Gel slices of ∼300 and ∼500 bp fragments were isolated and purified (Qiagen Gel extraction kit, see Subheading 3.4, step 5). ( b ) Paired-end libraries were constructed as described in the methods from the 300- and 500-bp fractions and amplified with 12 cycles of PCR, yielding barely visible bands. Note presence of adapters and PCR primers below the 100 bp marker. ( c ) Test for library complexity. One simple test to show that libraries contain predominantly genomic DNA and are not enriched for adapter dimers or other spurious overamplified bands is to digest the DyNAzyme-amplified libraries with Dpn II. This cleaves most of the adapter off the inserts. If genomic DNA has been cloned it will result in a smear (similar to genomic DNA digested for Southern blots). If only low complexity samples have been cloned in the library, sharp banding is observed instead of the smear and the library is unsuitable for further processing. ( d ) Libraries were amplified with 18 cycles of PCR with Phusion Flash High-Fidelity polymerase and purified (Qiagen PCR purification kit; see three 300-bp library samples). We typically pool three independent 25 μmL PCR reactions before purification and run 5 μL of 35 μL to show that only expected bands are obtained. Note the absence of the adapters or PCR primers and primer dimers (compare to ( b )).

    Article Snippet:Phusion Flash master mix: 1 unit/μL Phusion Flash High-Fidelity polymerase, 50 mM TAPS-HCl (pH 9.3), 100 mM KCl, 3 mM MgCl2 , 2 mM β-mercaptoethanol, 400 μM of dATP, dCTP, dGTP, and dTTP (NEB).

    Techniques: Sequencing, Sonication, Polymerase Chain Reaction, Purification, Agarose Gel Electrophoresis, Isolation, Gel Extraction, Construct, Amplification, Marker, Clone Assay