peg 8000  (New England Biolabs)


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    Structured Review

    New England Biolabs peg 8000
    Peg 8000, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/peg 8000/product/New England Biolabs
    Average 91 stars, based on 20 article reviews
    Price from $9.99 to $1999.99
    peg 8000 - by Bioz Stars, 2020-08
    91/100 stars

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    Polymerase Chain Reaction:

    Article Title: Cell type-specific profiling of protein-DNA interactions without cell isolation using Targeted DamID with next-generation sequencing
    Article Snippet: .. ▲ CRITICAL STEP A polymerase with hotstart is required to prevent primer dimer formation during PCR AlwI (NEB, cat. no. R0513S) RNase A (DNase-free) (Roche, cat. no. 11119915001) diluted to 12.5μg/ml Qubit assay tubes (Invitrogen, cat. no. ) Qubit dsDNA HS assay kit, (Invitrogen, cat. no. ) Agilent reagents for TapeStation: Genomic DNA ScreenTape(5067-5365) and reagents (5067-5366) Agilent reagents for Bioanalyzer:Agilent DNA 1000 Kit (5067-1504) Agencourt AMPure XP Beads (Beckman Coulter, cat. no. A63880) (Seramag SpeedBeads, 3 EDAC/PA5 (Fisher Scientific, cat. no. 12326433) prepared using the method of Rohland and Reich, 2012 with 20%(w/v) PEG-8000 are a cost-effective alternative to AMPure XP beads) Quick ligase (NEB, cat. no. M2200S) T4 DNA ligase (400,000U/ml) and 10x buffer (NEB, cat. no. M0202S) T4 DNA polymerase (NEB, cat. no. M0203S) Klenow Fragment (NEB, cat. no. M0210S) Klenow 3' to 5' exo- (NEB, cat. no. M0541S) T4 polynucleotide kinase (NEB, cat. no. M0201S) NEBNext High-Fidelity 2X PCR Master Mix (NEB, cat. no. M0541S) dNTPs (NEB, cat. no. N0446S) .. Temperature controlled heat block capable of heating to 95°C.

    Gel Extraction:

    Article Title: Candidate new rotavirus species in Schreiber's bats, Serbia.
    Article Snippet: .. In brief, 5 μL total RNA was combined with 25 μL RNA ligation mixture (consisting of 3.5 μL nuclease free water, 2 μL of 20 μM PC3, 12.5 μL of 34% (w/v) polyethylene glycol 8000, 3 μL of 10 mM ATP, 3 μL 10× T4 RNA Ligase buffer and 10 U T4 RNA Ligase I (New England Biolabs) and then incubated at 17°C for 16 h. Following the incubation, the RNA was extracted using the QIAquick Gel Extraction Kit (QIAGEN). .. Binding of RNA to silica-gel column was performed in the presence of 150 μL QG buffer from the extraction kit and 180 μL isopropanol.

    Incubation:

    Article Title: Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with repressed chromatin compartment and reveals transcription dynamics
    Article Snippet: .. For this purpose, bead-nuclei were resuspended in 190 µL RNA ligase solution (1× RNA ligase buffer (NEB), 4.5 µM bridge adapter, 20% PEG-8000 (NEB)), 10 µL T4 RNA ligase 2 truncated (200 U/µL, NEB) was added, and the mixture was incubated for 6 h at room temperature then overnight at 16 °C with shaking at 800 rpm. .. To wash off non-ligated bridge adapter, bead-nuclei were pelleted, resuspended in 200 µL nuclease-free water and mixed with 165 µL AMPure buffer (20% PEG-8000, 2.5 M NaCl) ( ).

    Article Title: A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos
    Article Snippet: .. The reaction was placed in a thermocycler preheated to 95 °C, incubated for 3 min, and then cold shocked on ice for at least 2 min. On ice, 1 pmol of the forward and 1 pmol of the reverse SRSLY adapters were added to the denaturation reaction, as well as PEG-8000, T4 DNA ligase Buffer, T4 PNK, and T4 DNA ligase (all New England Biolabs) to a final volume of 50 μl. .. PEG-8000 was added to a final concentration of 18.5% v/v.

    Article Title: Candidate new rotavirus species in Schreiber's bats, Serbia.
    Article Snippet: .. In brief, 5 μL total RNA was combined with 25 μL RNA ligation mixture (consisting of 3.5 μL nuclease free water, 2 μL of 20 μM PC3, 12.5 μL of 34% (w/v) polyethylene glycol 8000, 3 μL of 10 mM ATP, 3 μL 10× T4 RNA Ligase buffer and 10 U T4 RNA Ligase I (New England Biolabs) and then incubated at 17°C for 16 h. Following the incubation, the RNA was extracted using the QIAquick Gel Extraction Kit (QIAGEN). .. Binding of RNA to silica-gel column was performed in the presence of 150 μL QG buffer from the extraction kit and 180 μL isopropanol.

    Ligation:

    Article Title: Candidate new rotavirus species in Schreiber's bats, Serbia.
    Article Snippet: .. In brief, 5 μL total RNA was combined with 25 μL RNA ligation mixture (consisting of 3.5 μL nuclease free water, 2 μL of 20 μM PC3, 12.5 μL of 34% (w/v) polyethylene glycol 8000, 3 μL of 10 mM ATP, 3 μL 10× T4 RNA Ligase buffer and 10 U T4 RNA Ligase I (New England Biolabs) and then incubated at 17°C for 16 h. Following the incubation, the RNA was extracted using the QIAquick Gel Extraction Kit (QIAGEN). .. Binding of RNA to silica-gel column was performed in the presence of 150 μL QG buffer from the extraction kit and 180 μL isopropanol.

    Article Title: Integrated analysis of directly captured microRNA targets reveals the impact of microRNAs on mammalian transcriptome
    Article Snippet: .. Next, 3’ adapter ligation was performed on beads overnight in 40 ul of mixture: 17ul H2O, 4ul 10X T4 RNA ligase buffer (NEB), 1ul of 3’linker (5’-Adenylated & 3’ blocked - custom ordered from IDT), 16ul 50% PEG-8000, 1 ul RNaseOUT and 1ul T4 RNA ligase 2 truncated K227Q (NEB M0351). ..

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    New England Biolabs t4 rna ligase
    Amplification of anchor-ligated cDNAs is dependent on <t>T4</t> RNA ligase. Maize mitochondrial RNA (1–2 µg) was incubated with 40 pmol of anchor oligonucleotide in the presence or absence of T4 RNA ligase. Anchor-ligated RNAs were reverse transcribed and amplified by PCR and the cDNA products were electrophoresed on agarose gels. Lanes marked M show the migration of commercial DNA size markers. PCR products for the following cDNAs are shown: ( A ) atp9 , lanes 1 and 2; ( B ) cox2 , lanes 3 and 4; ( C ) rps12 , lanes 5 and 6, and trnS , lanes 7 and 8. Amplification of anchor-ligated atp9 . Odd numbered lanes (1, 3, 5 and 7) included T4 RNA ligase and even numbered lanes (2, 4, 6 and 8) omitted T4 RNA ligase.
    T4 Rna Ligase, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t4 rna ligase/product/New England Biolabs
    Average 99 stars, based on 30 article reviews
    Price from $9.99 to $1999.99
    t4 rna ligase - by Bioz Stars, 2020-08
    99/100 stars
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    99
    New England Biolabs t5 exonuclease
    The schematic of the TEDA method. The blue half-moon represents T5 exonuclease. The double lined rectangle with a gap represents a linearized plasmid. The double vertical lines represent the insert DNA. Lines with same color indicate the homologous region. Step 1: <t>T5</t> exonuclease cuts from the 5′ ends of linearized plasmid and insert DNA to generate 5′-overhangs. Step 2: the 5′-overhangs anneal to each other. Step 3: The cyclized DNA with DNA gaps is transformed into cells and the gaps are repaired in vivo .
    T5 Exonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t5 exonuclease/product/New England Biolabs
    Average 99 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    t5 exonuclease - by Bioz Stars, 2020-08
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    91
    New England Biolabs peg 8000
    The schematic of the TEDA method. The blue half-moon represents T5 exonuclease. The double lined rectangle with a gap represents a linearized plasmid. The double vertical lines represent the insert DNA. Lines with same color indicate the homologous region. Step 1: <t>T5</t> exonuclease cuts from the 5′ ends of linearized plasmid and insert DNA to generate 5′-overhangs. Step 2: the 5′-overhangs anneal to each other. Step 3: The cyclized DNA with DNA gaps is transformed into cells and the gaps are repaired in vivo .
    Peg 8000, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 20 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/peg 8000/product/New England Biolabs
    Average 91 stars, based on 20 article reviews
    Price from $9.99 to $1999.99
    peg 8000 - by Bioz Stars, 2020-08
    91/100 stars
      Buy from Supplier

    Image Search Results


    Amplification of anchor-ligated cDNAs is dependent on T4 RNA ligase. Maize mitochondrial RNA (1–2 µg) was incubated with 40 pmol of anchor oligonucleotide in the presence or absence of T4 RNA ligase. Anchor-ligated RNAs were reverse transcribed and amplified by PCR and the cDNA products were electrophoresed on agarose gels. Lanes marked M show the migration of commercial DNA size markers. PCR products for the following cDNAs are shown: ( A ) atp9 , lanes 1 and 2; ( B ) cox2 , lanes 3 and 4; ( C ) rps12 , lanes 5 and 6, and trnS , lanes 7 and 8. Amplification of anchor-ligated atp9 . Odd numbered lanes (1, 3, 5 and 7) included T4 RNA ligase and even numbered lanes (2, 4, 6 and 8) omitted T4 RNA ligase.

    Journal: Nucleic Acids Research

    Article Title: Addition of non-genomically encoded nucleotides to the 3?-terminus of maize mitochondrial mRNAs: truncated rps12 mRNAs frequently terminate with CCA

    doi:

    Figure Lengend Snippet: Amplification of anchor-ligated cDNAs is dependent on T4 RNA ligase. Maize mitochondrial RNA (1–2 µg) was incubated with 40 pmol of anchor oligonucleotide in the presence or absence of T4 RNA ligase. Anchor-ligated RNAs were reverse transcribed and amplified by PCR and the cDNA products were electrophoresed on agarose gels. Lanes marked M show the migration of commercial DNA size markers. PCR products for the following cDNAs are shown: ( A ) atp9 , lanes 1 and 2; ( B ) cox2 , lanes 3 and 4; ( C ) rps12 , lanes 5 and 6, and trnS , lanes 7 and 8. Amplification of anchor-ligated atp9 . Odd numbered lanes (1, 3, 5 and 7) included T4 RNA ligase and even numbered lanes (2, 4, 6 and 8) omitted T4 RNA ligase.

    Article Snippet: The ligation reactions contained 50 mM Tris–HCl, pH 8.0, 10 mM MgCl2 , 0.2 mg/ml BSA, 1 mM hexamine cobalt chloride, 20 µM ATP, 12.5% PEG 8000 and 15 U T4 RNA ligase (New England Biolabs).

    Techniques: Amplification, Incubation, Polymerase Chain Reaction, Migration

    The schematic of the TEDA method. The blue half-moon represents T5 exonuclease. The double lined rectangle with a gap represents a linearized plasmid. The double vertical lines represent the insert DNA. Lines with same color indicate the homologous region. Step 1: T5 exonuclease cuts from the 5′ ends of linearized plasmid and insert DNA to generate 5′-overhangs. Step 2: the 5′-overhangs anneal to each other. Step 3: The cyclized DNA with DNA gaps is transformed into cells and the gaps are repaired in vivo .

    Journal: Nucleic Acids Research

    Article Title: T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis

    doi: 10.1093/nar/gky1169

    Figure Lengend Snippet: The schematic of the TEDA method. The blue half-moon represents T5 exonuclease. The double lined rectangle with a gap represents a linearized plasmid. The double vertical lines represent the insert DNA. Lines with same color indicate the homologous region. Step 1: T5 exonuclease cuts from the 5′ ends of linearized plasmid and insert DNA to generate 5′-overhangs. Step 2: the 5′-overhangs anneal to each other. Step 3: The cyclized DNA with DNA gaps is transformed into cells and the gaps are repaired in vivo .

    Article Snippet: For optimization, PEG 8000 and the proper dilution of T5 exonuclease were two key factors for TEDA (Figure ).

    Techniques: Plasmid Preparation, Transformation Assay, In Vivo

    Enzymes and buffer components required for TEDA. ( A ) The pKat-eGFP fragment was cloned into SmaI-digested pBluescript SK–. The assembly of the two fragments was used as a model for the test. ( B ) Taq DNA ligase, Phusion DNA polymerase, T5 exonuclease (T5 exo), NAD + were tested for their necessity for the DNA assembly. In addition, Prime-STAR or FastPfu was also used instead of Phusion for testing; ( C ) PEG 8000 and dNTPs were further tested for their necessity for the DNA assembly. The concentrations of relevant components mentioned above were indicated in the figure. The base solution contained 0.1 M Tris–HCl (pH 7.5), 10 mM MgCl 2 and 10 mM dithiothreitol. The reaction was processed at 50°C for 1 h, which was the same as the Gibson assembly. *, Gibson; **, Hot Fusion; **, TEDA with dNTPs and at 50°C; ****, TEDA without dNTPs at 50°C. The data are averages of three parallel experiments with STDEV.

    Journal: Nucleic Acids Research

    Article Title: T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis

    doi: 10.1093/nar/gky1169

    Figure Lengend Snippet: Enzymes and buffer components required for TEDA. ( A ) The pKat-eGFP fragment was cloned into SmaI-digested pBluescript SK–. The assembly of the two fragments was used as a model for the test. ( B ) Taq DNA ligase, Phusion DNA polymerase, T5 exonuclease (T5 exo), NAD + were tested for their necessity for the DNA assembly. In addition, Prime-STAR or FastPfu was also used instead of Phusion for testing; ( C ) PEG 8000 and dNTPs were further tested for their necessity for the DNA assembly. The concentrations of relevant components mentioned above were indicated in the figure. The base solution contained 0.1 M Tris–HCl (pH 7.5), 10 mM MgCl 2 and 10 mM dithiothreitol. The reaction was processed at 50°C for 1 h, which was the same as the Gibson assembly. *, Gibson; **, Hot Fusion; **, TEDA with dNTPs and at 50°C; ****, TEDA without dNTPs at 50°C. The data are averages of three parallel experiments with STDEV.

    Article Snippet: For optimization, PEG 8000 and the proper dilution of T5 exonuclease were two key factors for TEDA (Figure ).

    Techniques: Clone Assay

    Comparison of different assembly methods. ( A ) TEDA was compared with In-fusion and SLIC for the assembly of two fragments. Middle- lacZ and pBBR1MCS5::lacZ-truncated with 15-bp or 20-bp overlaps were used. 1:1, the same molar ratio of the insert to vector was used for DNA assembly; 1:2, double molar amount of the insert to vector was used for DNA assembly. ( B ) TEDA was compared with Gibson and non-optimized TEDA methods. The Pkat-eGFP and SmaI-pSK was used for cloning. TEDA(0.04U)−30°C, 0.04 U T5 exonuclease at 30°C for 40 min; TEDA(0.08 U)−30°C, 0.08 U T5 exonuclease at 30°C for 40 min; TEDA(0.04 U)−50°C, 0.04 U T5 exonuclease at 50°C for 40 min; Gibson, 0.08 U T5 exonuclease with Phusion and Taq DNA ligase at 50°C for 60 min. Neg, DNA fragments were transformed without TEDA treatment. ( C ) TEDA was compared with In-fusion for 4 fragments assembly. The 5Ptac-phbCAB operon was separated into three fragments (Figure 2A ), and they were assembled with linearized pBBR1MCS-2 to generate pBBR1MCS2::5Ptac-phbCAB. The data are averages of three parallel experiments with STDEV.

    Journal: Nucleic Acids Research

    Article Title: T5 exonuclease-dependent assembly offers a low-cost method for efficient cloning and site-directed mutagenesis

    doi: 10.1093/nar/gky1169

    Figure Lengend Snippet: Comparison of different assembly methods. ( A ) TEDA was compared with In-fusion and SLIC for the assembly of two fragments. Middle- lacZ and pBBR1MCS5::lacZ-truncated with 15-bp or 20-bp overlaps were used. 1:1, the same molar ratio of the insert to vector was used for DNA assembly; 1:2, double molar amount of the insert to vector was used for DNA assembly. ( B ) TEDA was compared with Gibson and non-optimized TEDA methods. The Pkat-eGFP and SmaI-pSK was used for cloning. TEDA(0.04U)−30°C, 0.04 U T5 exonuclease at 30°C for 40 min; TEDA(0.08 U)−30°C, 0.08 U T5 exonuclease at 30°C for 40 min; TEDA(0.04 U)−50°C, 0.04 U T5 exonuclease at 50°C for 40 min; Gibson, 0.08 U T5 exonuclease with Phusion and Taq DNA ligase at 50°C for 60 min. Neg, DNA fragments were transformed without TEDA treatment. ( C ) TEDA was compared with In-fusion for 4 fragments assembly. The 5Ptac-phbCAB operon was separated into three fragments (Figure 2A ), and they were assembled with linearized pBBR1MCS-2 to generate pBBR1MCS2::5Ptac-phbCAB. The data are averages of three parallel experiments with STDEV.

    Article Snippet: For optimization, PEG 8000 and the proper dilution of T5 exonuclease were two key factors for TEDA (Figure ).

    Techniques: Plasmid Preparation, Clone Assay, Transformation Assay