thermopol reaction buffer  (New England Biolabs)


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    Name:
    ThermoPol Reaction Buffer Pack
    Description:
    ThermoPol Reaction Buffer Pack 6 0 ml
    Catalog Number:
    b9004s
    Price:
    22
    Size:
    6 0 ml
    Category:
    Buffers
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    Structured Review

    New England Biolabs thermopol reaction buffer
    ThermoPol Reaction Buffer Pack
    ThermoPol Reaction Buffer Pack 6 0 ml
    https://www.bioz.com/result/thermopol reaction buffer/product/New England Biolabs
    Average 90 stars, based on 105 article reviews
    Price from $9.99 to $1999.99
    thermopol reaction buffer - by Bioz Stars, 2020-01
    90/100 stars

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    Related Articles

    Amplification:

    Article Title: Optimization of trans-Splicing for Huntington's Disease RNA Therapy
    Article Snippet: For amplifications outside the HTT exon 1 CAG repeat and the adjacent GC-rich region, Pfu enzyme (prepared in-house) with Thermopol buffer (New England Biolabs, B9004S) was used. .. For amplification across the exon 1 CAG repeat, Taq PCRx with 2 × enhancer solution (Invitrogen, 11495-017) was used, per manufacturer instructions.

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: The 25 µl reaction mixture contained 2.5 µl of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs, Hertfordshire, UK), 4 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 0.1 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), 1 µl each of 10 pmol/µl forward and reverse primer , 15.4 µl of sterile Milli-Q water, and 1 µl of DNA template. .. PCR amplification was carried out in an Eppendorf Master Cycler (22331, Eppendorf, Germany) using the following temperature program: initial denaturation (1 min, 94°C) followed by 35 cycles of denaturation (1 min, 94°C), annealing (1 min, 55°C), and elongation (1 min, 72°C) and then final extension (7 min, 72°C).

    Article Title: Association between Three Mutations, F1565C, V1023G and S996P, in the Voltage-Sensitive Sodium Channel Gene and Knockdown Resistance in Aedes aegypti from Yogyakarta, Indonesia
    Article Snippet: Amplicon size was 53 bp. .. For site 1565, the 10 μL PCR reaction contained 2 μL of 1 in 10 diluted template DNA, 0.4 μL each of the primers at 10 μM, 1 μL of the ThermoPol reaction buffer (NEB Inc., Ipswich, MA, USA; Cat. No. B9004S), 0.064 μL of dNTP’s at 25 mM (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-39029), 0.4 μL of MgCl2 (50 mM) (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-21047), 0.25 μL of the LightCycler® 480 High Resolution Melting Master (Roche, Mannheim, Germany; Cat. No. 04909631001), 0.01 μL of IMMOLASE™ DNA polymerase (10 u/μL) (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-21047) and 5.476 μL of ddH2 O (Honeywell, Burdick and Jackson; Muskegon, MI, USA; Cat. No. 365-4).

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: PCR amplification was carried out in an Eppendorf Master Cycler (22331, Eppendorf, Germany) using the following temperature program: initial denaturation (1 min, 94°C) followed by 35 cycles of denaturation (1 min, 94°C), annealing (1 min, 55°C), and elongation (1 min, 72°C) and then final extension (7 min, 72°C). .. The 50 µl PCR assay mix contained 32.8 µl of sterile Milli-Q water, 1 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 5 µL of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs), 3 µl each of 10 pmol/µl forward and reverse primer , 0.2 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), and 5 µl of DNA template.

    Article Title: Reasons for the Invasive Success of a Guppy (Poecilia reticulata) Population in Trinidad
    Article Snippet: .. For DNA amplification the following PCR protocol was used: 2.5 µl [25 ng/µl] template, 4.4 µl H2 O, 1 µl PCR buffer [10× Thermobuffer (NEB B9004S)], 1 µl dNTPs [2 mM], 0.1 µl Taq polymerase [5000 U/m (NEB M0267L)], 0.5 µl Fw-primer and 0.5 µl Rev-primer [both 10 pmol/µl]. .. All PCR amplifications run in Peltier Thermal Cyclers pTC-200 from Bio-Rad under the following conditions: 96°C for 3 min, 40 cycles of 96°C for 30 sec., 56°C for 30 sec., 68°C for 30 sec.; 68°C for 5 min.

    Article Title: Metabolomic Profiles of a Midge (Procladius villosimanus, Kieffer) Are Associated with Sediment Contamination in Urban Wetlands
    Article Snippet: Samples were then centrifuged for 5 min at 2700× g , supernatant diluted 1/50 and stored at −20 °C until PCR amplification. .. Each PCR reaction was 25 μL and contained the following components: 5 μL Chelex extracted DNA, 2.5 μL ThermoPol 10× buffer (New England Biolabs Ipswich, United States (NEB) Cat. No. B9004S), 2 min μL dNTP (25 mM), 0.2 μL Taq DNA polymerase (NEB Cat. No. M0273S), 1.25 μL each LCO1490 and HC02198 primers (10 μM each) and 12.8 μL of double deionized water.

    Article Title: A DNA nanoscope via auto-cycling proximity recording
    Article Snippet: After 30 min of incubation, unbound origami and extra staple strands were removed by washing three times with 60 μl of fresh TAE/Mg buffer (40 mM Tris acetate, 1 mM EDTA buffer supplemented with 12.5 mM magnesium acetate) and three times with 60 μl of 1× ThermoPol buffer (NEB, Cat. No. B9004S, 10× ; 1× contains 20 mM Tris-HCl, 10 mM (NH4 )2 SO4 , 10 mM KCl, 2 mM MgSO4 , 0.1% Triton X-100). .. This minimizes any false-positive PCR amplification by the recording primers.

    Article Title: Phenotypic and genotypic characteristics of Trueperellapyogenes isolated from ruminants
    Article Snippet: The pld -negative isolates were examined for 8 known and putative virulence genes, utilizing previously developed PCR protocols and primers., The PCR program was performed as follows : denaturation at 95°C for 4 min; 35 cycles of 94°C for 1 min, annealing for 30 s at different temperatures (60°C for nanH -, nanP -, plo -, cbpA -, and fimC -specific PCRs; and 57°C for fimA - and fimG -specific PCRs), , 72°C for 3 min; and a final extension at 72°C for 7 min. All amplifications were carried out in 50 µL of the following reaction mixture: 10 pmol of each primer (0.5 µL each), 10 mM of each dNTP (N0447S, New England BioLabs, Ipswich, MA), 1× Taq polymerase buffer (B9004S, New England BioLabs), 1 U of Taq DNA polymerase (M0273L, New England BioLabs), and ~50 ng of genomic DNA. .. A fragment of the 16S ribosomal (r)RNA gene was amplified utilizing the universal primers UNF (5’-GAGTTTGATCCTGGCTCAG-3’) and UNR (5’-GGACTACCAGGGTATCTAAT-3’) targeting bases 9–27 and 805–786 of the 16S rRNA gene of Escherichia coli , respectively.

    Synthesized:

    Article Title: Optimization of trans-Splicing for Huntington's Disease RNA Therapy
    Article Snippet: RNA was resuspended in 10 mM Tris–HCl pH 8.2, 1 mM EDTA, and concentrations were measured using a Nanodrop (Thermo Fisher). cDNA was synthesized using 1 μg of RNA and random primers following the SuperScript III protocol (Invitrogen, 18080-044). .. For amplifications outside the HTT exon 1 CAG repeat and the adjacent GC-rich region, Pfu enzyme (prepared in-house) with Thermopol buffer (New England Biolabs, B9004S) was used.

    Electrophoresis:

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: The 50 µl PCR assay mix contained 32.8 µl of sterile Milli-Q water, 1 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 5 µL of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs), 3 µl each of 10 pmol/µl forward and reverse primer , 0.2 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), and 5 µl of DNA template. .. All PCR amplicons were visualized by electrophoresis on 1% (1.2% for ITS-PCR) agarose gels containing 2 µl GelRed stain (41003, Biotium, Fremont, CA, USA); wells were loaded with 10 µl of PCR product + 2 µl of loading dye (R0611, Thermo Fisher Scientific, Loughborough, UK).

    Article Title: Phenotypic and genotypic characteristics of Trueperellapyogenes isolated from ruminants
    Article Snippet: The pld -negative isolates were examined for 8 known and putative virulence genes, utilizing previously developed PCR protocols and primers., The PCR program was performed as follows : denaturation at 95°C for 4 min; 35 cycles of 94°C for 1 min, annealing for 30 s at different temperatures (60°C for nanH -, nanP -, plo -, cbpA -, and fimC -specific PCRs; and 57°C for fimA - and fimG -specific PCRs), , 72°C for 3 min; and a final extension at 72°C for 7 min. All amplifications were carried out in 50 µL of the following reaction mixture: 10 pmol of each primer (0.5 µL each), 10 mM of each dNTP (N0447S, New England BioLabs, Ipswich, MA), 1× Taq polymerase buffer (B9004S, New England BioLabs), 1 U of Taq DNA polymerase (M0273L, New England BioLabs), and ~50 ng of genomic DNA. .. The PCR products were separated by electrophoresis through a 2% agarose gel in Tris–acetate–EDTA buffer (40 mM Tris, 20 mM acetic acid, 1 mM EDTA; Thermo Fisher Scientific, Lenexa, KS), stained with ethidium bromide (MilliporeSigma), and visualized using an Alpha Imager HP (Alpha-Innotech, San Leandro, CA).

    Incubation:

    Article Title: Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes
    Article Snippet: Up to 100 ng of each snRNA was decapped in a 10 µl reaction with 1x ThermoPol buffer (NEB B9004S) and 5U RppH (NEB M0356) for 2 hr at 37 °C. .. The reaction was supplemented with 2 µl 1U µl−1 Nuclease P1 (Sigma N8630) in a 30-µl reaction with 0.2 mM ZnCl2 and 20 mM NH4 OAc pH 5.3, incubated for 2 hr at 42 °C.

    Article Title: ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition
    Article Snippet: .. The mixture was incubated at 37°C for an additional 5 h. For quantification of cap m6 Am , 100 ng poly(A) RNA was decapped with 20 units of RNA 5′pyrophosphohydrolase (RppH; M0356; New England Biolabs) in 1×Thermopol buffer (B9004S; New England Biolabs) for 3 h at 37°C, and then treated with Nuclease P1 and alkaline phosphatase as described above. ..

    Article Title: A DNA nanoscope via auto-cycling proximity recording
    Article Snippet: .. After 30 min of incubation, unbound origami and extra staple strands were removed by washing three times with 60 μl of fresh TAE/Mg buffer (40 mM Tris acetate, 1 mM EDTA buffer supplemented with 12.5 mM magnesium acetate) and three times with 60 μl of 1× ThermoPol buffer (NEB, Cat. No. B9004S, 10× ; 1× contains 20 mM Tris-HCl, 10 mM (NH4 )2 SO4 , 10 mM KCl, 2 mM MgSO4 , 0.1% Triton X-100). .. To the chamber, a 40 μl solution containing 0.8 units/μl of Bst polymerase (NEB, Cat. No. M0275S), 100 μM dNTP (NEB, Cat. No. N0447S), and the relevant primer mixes typically at 100 nM each, in 1× ThermoPol reaction buffer, was added and incubated for 1 h at room temperature.

    Mass Spectrometry:

    Article Title: ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition
    Article Snippet: The mixture was incubated at 37°C for an additional 5 h. For quantification of cap m6 Am , 100 ng poly(A) RNA was decapped with 20 units of RNA 5′pyrophosphohydrolase (RppH; M0356; New England Biolabs) in 1×Thermopol buffer (B9004S; New England Biolabs) for 3 h at 37°C, and then treated with Nuclease P1 and alkaline phosphatase as described above. .. The nucleosides were separated by UPLC (Shimadzu) equipped with a ZORBAX SB-Aq column (Agilent) and detected by MS/MS using a Triple Quad 5500 (AB SCIEX) mass spectrometer in positive ion mode by multiple reaction monitoring.

    Article Title: Phenotypic and genotypic characteristics of Trueperellapyogenes isolated from ruminants
    Article Snippet: The pld -negative isolates were examined for 8 known and putative virulence genes, utilizing previously developed PCR protocols and primers., The PCR program was performed as follows : denaturation at 95°C for 4 min; 35 cycles of 94°C for 1 min, annealing for 30 s at different temperatures (60°C for nanH -, nanP -, plo -, cbpA -, and fimC -specific PCRs; and 57°C for fimA - and fimG -specific PCRs), , 72°C for 3 min; and a final extension at 72°C for 7 min. All amplifications were carried out in 50 µL of the following reaction mixture: 10 pmol of each primer (0.5 µL each), 10 mM of each dNTP (N0447S, New England BioLabs, Ipswich, MA), 1× Taq polymerase buffer (B9004S, New England BioLabs), 1 U of Taq DNA polymerase (M0273L, New England BioLabs), and ~50 ng of genomic DNA. .. The pld -negative isolates were examined for 8 known and putative virulence genes, utilizing previously developed PCR protocols and primers., The PCR program was performed as follows : denaturation at 95°C for 4 min; 35 cycles of 94°C for 1 min, annealing for 30 s at different temperatures (60°C for nanH -, nanP -, plo -, cbpA -, and fimC -specific PCRs; and 57°C for fimA - and fimG -specific PCRs), , 72°C for 3 min; and a final extension at 72°C for 7 min. All amplifications were carried out in 50 µL of the following reaction mixture: 10 pmol of each primer (0.5 µL each), 10 mM of each dNTP (N0447S, New England BioLabs, Ipswich, MA), 1× Taq polymerase buffer (B9004S, New England BioLabs), 1 U of Taq DNA polymerase (M0273L, New England BioLabs), and ~50 ng of genomic DNA.

    Genome Wide:

    Article Title: Reasons for the Invasive Success of a Guppy (Poecilia reticulata) Population in Trinidad
    Article Snippet: Here population specific markers already existed due to a genome-wide SNP study of guppy population history in Trinidad and Venezuela . .. For DNA amplification the following PCR protocol was used: 2.5 µl [25 ng/µl] template, 4.4 µl H2 O, 1 µl PCR buffer [10× Thermobuffer (NEB B9004S)], 1 µl dNTPs [2 mM], 0.1 µl Taq polymerase [5000 U/m (NEB M0267L)], 0.5 µl Fw-primer and 0.5 µl Rev-primer [both 10 pmol/µl].

    Modification:

    Article Title: ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition
    Article Snippet: Paragraph title: Quantitative Analysis of RNA Modification by LC-MS/MS ... The mixture was incubated at 37°C for an additional 5 h. For quantification of cap m6 Am , 100 ng poly(A) RNA was decapped with 20 units of RNA 5′pyrophosphohydrolase (RppH; M0356; New England Biolabs) in 1×Thermopol buffer (B9004S; New England Biolabs) for 3 h at 37°C, and then treated with Nuclease P1 and alkaline phosphatase as described above.

    Countercurrent Chromatography:

    Article Title: Association between Three Mutations, F1565C, V1023G and S996P, in the Voltage-Sensitive Sodium Channel Gene and Knockdown Resistance in Aedes aegypti from Yogyakarta, Indonesia
    Article Snippet: The non-synonymous mutation occurs in the first codon position, changing serine (TCC) to proline (CCC) [ ]. .. For site 1565, the 10 μL PCR reaction contained 2 μL of 1 in 10 diluted template DNA, 0.4 μL each of the primers at 10 μM, 1 μL of the ThermoPol reaction buffer (NEB Inc., Ipswich, MA, USA; Cat. No. B9004S), 0.064 μL of dNTP’s at 25 mM (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-39029), 0.4 μL of MgCl2 (50 mM) (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-21047), 0.25 μL of the LightCycler® 480 High Resolution Melting Master (Roche, Mannheim, Germany; Cat. No. 04909631001), 0.01 μL of IMMOLASE™ DNA polymerase (10 u/μL) (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-21047) and 5.476 μL of ddH2 O (Honeywell, Burdick and Jackson; Muskegon, MI, USA; Cat. No. 365-4).

    Flow Cytometry:

    Article Title: A DNA nanoscope via auto-cycling proximity recording
    Article Snippet: For recording reactions on origami, flow chambers were created by attaching a freshly cleaved mica (Ted Pella) piece to a channel slide system (ibidi, Sticky-Slide VI0.4, Cat. No. 80608), yielding a 30 μl chamber volume. .. After 30 min of incubation, unbound origami and extra staple strands were removed by washing three times with 60 μl of fresh TAE/Mg buffer (40 mM Tris acetate, 1 mM EDTA buffer supplemented with 12.5 mM magnesium acetate) and three times with 60 μl of 1× ThermoPol buffer (NEB, Cat. No. B9004S, 10× ; 1× contains 20 mM Tris-HCl, 10 mM (NH4 )2 SO4 , 10 mM KCl, 2 mM MgSO4 , 0.1% Triton X-100).

    Ligation:

    Article Title: Single-molecule nascent RNA sequencing reveals regulatory domain architecture at promoters and enhancers
    Article Snippet: The three cap state selections use a series of enzymatic treatments to reduce specific populations of RNAs to 5’ monophosphate, making them capable of ligation to an RNA adapter by T4 RNA ligase (NEB, cat. M0204S). .. 5’ cap was removed with RNA 5’ pyrophosphohydrolase, RppH (NEB, cat. M0356S), using ThermoPol buffer (NEB, cat. B9004S).

    Cell Culture:

    Article Title: Single-molecule nascent RNA sequencing reveals regulatory domain architecture at promoters and enhancers
    Article Snippet: Paragraph title: Cell Culture and CoPRO library preparation ... 5’ cap was removed with RNA 5’ pyrophosphohydrolase, RppH (NEB, cat. M0356S), using ThermoPol buffer (NEB, cat. B9004S).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Optimization of trans-Splicing for Huntington's Disease RNA Therapy
    Article Snippet: Paragraph title: RNA isolation and RT-PCR ... For amplifications outside the HTT exon 1 CAG repeat and the adjacent GC-rich region, Pfu enzyme (prepared in-house) with Thermopol buffer (New England Biolabs, B9004S) was used.

    Tandem Mass Spectroscopy:

    Article Title: ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition
    Article Snippet: The mixture was incubated at 37°C for an additional 5 h. For quantification of cap m6 Am , 100 ng poly(A) RNA was decapped with 20 units of RNA 5′pyrophosphohydrolase (RppH; M0356; New England Biolabs) in 1×Thermopol buffer (B9004S; New England Biolabs) for 3 h at 37°C, and then treated with Nuclease P1 and alkaline phosphatase as described above. .. The nucleosides were separated by UPLC (Shimadzu) equipped with a ZORBAX SB-Aq column (Agilent) and detected by MS/MS using a Triple Quad 5500 (AB SCIEX) mass spectrometer in positive ion mode by multiple reaction monitoring.

    Sequencing:

    Article Title: Metabolomic Profiles of a Midge (Procladius villosimanus, Kieffer) Are Associated with Sediment Contamination in Urban Wetlands
    Article Snippet: Procladius species were identified by amplifying and sequencing a 710 bp fragment of the COI gene using the universal primers LCO1490: 5′-ggtcaacaaatcataaagatattgg-3′ and HC02198: 5′-taaacttcagggtgaccaaaaaatca-3′ Folmer, et al. [ ]. .. Each PCR reaction was 25 μL and contained the following components: 5 μL Chelex extracted DNA, 2.5 μL ThermoPol 10× buffer (New England Biolabs Ipswich, United States (NEB) Cat. No. B9004S), 2 min μL dNTP (25 mM), 0.2 μL Taq DNA polymerase (NEB Cat. No. M0273S), 1.25 μL each LCO1490 and HC02198 primers (10 μM each) and 12.8 μL of double deionized water.

    Recombinant:

    Article Title: Base-Pair Resolution Genome-Wide Mapping Of Active RNA polymerases using Precision Nuclear Run-On (PRO-seq)
    Article Snippet: Paragraph title: Enzymes and recombinant protein reagents ... Alternatively, RNA 5′ Pyrophosphohydrolase, 5 units/μl (RppH) (NEB, cat. no. M0356S) can be used with ThermoPol Reaction buffer (NEB, cat. no. B9004S).

    Nucleic Acid Electrophoresis:

    Article Title: Metabolomic Profiles of a Midge (Procladius villosimanus, Kieffer) Are Associated with Sediment Contamination in Urban Wetlands
    Article Snippet: Each PCR reaction was 25 μL and contained the following components: 5 μL Chelex extracted DNA, 2.5 μL ThermoPol 10× buffer (New England Biolabs Ipswich, United States (NEB) Cat. No. B9004S), 2 min μL dNTP (25 mM), 0.2 μL Taq DNA polymerase (NEB Cat. No. M0273S), 1.25 μL each LCO1490 and HC02198 primers (10 μM each) and 12.8 μL of double deionized water. .. Amplification bands of correct size were confirmed with gel electrophoresis, using 2% agarose gels, stained with sybr safe (Thermo Fisher Scientific Cat No.: S33102).

    Fluorescence:

    Article Title: Association between Three Mutations, F1565C, V1023G and S996P, in the Voltage-Sensitive Sodium Channel Gene and Knockdown Resistance in Aedes aegypti from Yogyakarta, Indonesia
    Article Snippet: For site 1565, the 10 μL PCR reaction contained 2 μL of 1 in 10 diluted template DNA, 0.4 μL each of the primers at 10 μM, 1 μL of the ThermoPol reaction buffer (NEB Inc., Ipswich, MA, USA; Cat. No. B9004S), 0.064 μL of dNTP’s at 25 mM (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-39029), 0.4 μL of MgCl2 (50 mM) (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-21047), 0.25 μL of the LightCycler® 480 High Resolution Melting Master (Roche, Mannheim, Germany; Cat. No. 04909631001), 0.01 μL of IMMOLASE™ DNA polymerase (10 u/μL) (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-21047) and 5.476 μL of ddH2 O (Honeywell, Burdick and Jackson; Muskegon, MI, USA; Cat. No. 365-4). .. Thermo cycling steps were: 95 °C for 10 min, 20 cycles of 95 °C for 5 s, 65 °C (reduce 0.5 °C each cycle) for 15 s, 72 °C for 15 s, followed by an additional 20 cycles of 95 °C for 5 s, 55 °C for 15 s, and 72 °C for 15 s. Fluorescence information was captured at the end of each 72 °C step.

    Methylation:

    Article Title: Single-molecule nascent RNA sequencing reveals regulatory domain architecture at promoters and enhancers
    Article Snippet: 5’ cap was removed with RNA 5’ pyrophosphohydrolase, RppH (NEB, cat. M0356S), using ThermoPol buffer (NEB, cat. B9004S). .. It is not sensitive to the subsequent methylation step of capping .

    Mutagenesis:

    Article Title: Association between Three Mutations, F1565C, V1023G and S996P, in the Voltage-Sensitive Sodium Channel Gene and Knockdown Resistance in Aedes aegypti from Yogyakarta, Indonesia
    Article Snippet: The non-synonymous mutation occurs in the first codon position, changing serine (TCC) to proline (CCC) [ ]. .. For site 1565, the 10 μL PCR reaction contained 2 μL of 1 in 10 diluted template DNA, 0.4 μL each of the primers at 10 μM, 1 μL of the ThermoPol reaction buffer (NEB Inc., Ipswich, MA, USA; Cat. No. B9004S), 0.064 μL of dNTP’s at 25 mM (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-39029), 0.4 μL of MgCl2 (50 mM) (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-21047), 0.25 μL of the LightCycler® 480 High Resolution Melting Master (Roche, Mannheim, Germany; Cat. No. 04909631001), 0.01 μL of IMMOLASE™ DNA polymerase (10 u/μL) (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-21047) and 5.476 μL of ddH2 O (Honeywell, Burdick and Jackson; Muskegon, MI, USA; Cat. No. 365-4).

    Isolation:

    Article Title: Optimization of trans-Splicing for Huntington's Disease RNA Therapy
    Article Snippet: Paragraph title: RNA isolation and RT-PCR ... For amplifications outside the HTT exon 1 CAG repeat and the adjacent GC-rich region, Pfu enzyme (prepared in-house) with Thermopol buffer (New England Biolabs, B9004S) was used.

    Article Title: Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes
    Article Snippet: Paragraph title: snRNA isolation and nucleoside UHPLC-MS/MS ... Up to 100 ng of each snRNA was decapped in a 10 µl reaction with 1x ThermoPol buffer (NEB B9004S) and 5U RppH (NEB M0356) for 2 hr at 37 °C.

    Article Title: Efficient and Specific Detection of Salmonella in Food Samples Using a stn-Based Loop-Mediated Isothermal Amplification Method
    Article Snippet: LAMP Reaction and LAMP Product Detection The LAMP reaction was performed in a total volume of 25 μ L containing the following components (final concentration): 1.6 μ M each of FIP and BIP primers, 0.2 μ M each of F3 and B3 primers, 0.8 μ M each of LF and LB primers (in the same LAMP reaction), 1.6 mM of deoxyribonucleotide triphosphate mixture (dNTPs), 1 M betaine (Sigma, B2629, St. Louis, USA), 6 mM MgSO4 , 1x thermopol buffer (New England Biolabs, B9004S, Beverly, USA), 1 μ L (8 U) of B st DNA polymerase large fragment (New England Biolabs, M0275S, Beverly, USA), and 5 μ L of DNA template solution. .. Typhimurium ATCC 23566 cells or its isolated DNA (1 ng/reaction) was used as positive controls.

    Article Title: Reasons for the Invasive Success of a Guppy (Poecilia reticulata) Population in Trinidad
    Article Snippet: DNA was isolated using the DNeasy Blood & Tissue Kit from Qiagen. .. For DNA amplification the following PCR protocol was used: 2.5 µl [25 ng/µl] template, 4.4 µl H2 O, 1 µl PCR buffer [10× Thermobuffer (NEB B9004S)], 1 µl dNTPs [2 mM], 0.1 µl Taq polymerase [5000 U/m (NEB M0267L)], 0.5 µl Fw-primer and 0.5 µl Rev-primer [both 10 pmol/µl].

    Size-exclusion Chromatography:

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: The 50 µl PCR assay mix contained 32.8 µl of sterile Milli-Q water, 1 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 5 µL of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs), 3 µl each of 10 pmol/µl forward and reverse primer , 0.2 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), and 5 µl of DNA template. .. PCR amplification was carried out using the following temperature program: initial denaturation (5 min, 95°C) followed by 25 cycles of denaturation (45 sec, 94°C), annealing (1 min, at primer-specific temperature [ ]), and elongation (1 min, 72°C) and then final extension (10 min, 72°C).

    Article Title: Reasons for the Invasive Success of a Guppy (Poecilia reticulata) Population in Trinidad
    Article Snippet: For DNA amplification the following PCR protocol was used: 2.5 µl [25 ng/µl] template, 4.4 µl H2 O, 1 µl PCR buffer [10× Thermobuffer (NEB B9004S)], 1 µl dNTPs [2 mM], 0.1 µl Taq polymerase [5000 U/m (NEB M0267L)], 0.5 µl Fw-primer and 0.5 µl Rev-primer [both 10 pmol/µl]. .. All PCR amplifications run in Peltier Thermal Cyclers pTC-200 from Bio-Rad under the following conditions: 96°C for 3 min, 40 cycles of 96°C for 30 sec., 56°C for 30 sec., 68°C for 30 sec.; 68°C for 5 min.

    Purification:

    Article Title: Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes
    Article Snippet: U1/5.8s-rRNA and U4 snRNAs were purified by cutting out the 164nt and 141nt bands respectively, using the low-range ssRNA ladder as a size marker (NEB N0364). snRNAs were gel eluted in elution buffer [0.4 M NaCl, 10 mM Tris pH 7.5, 1 mM EDTA pH 8] at 16 °C overnight with shaking at 2000 rpm. .. Up to 100 ng of each snRNA was decapped in a 10 µl reaction with 1x ThermoPol buffer (NEB B9004S) and 5U RppH (NEB M0356) for 2 hr at 37 °C.

    Polymerase Chain Reaction:

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: .. The 25 µl reaction mixture contained 2.5 µl of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs, Hertfordshire, UK), 4 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 0.1 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), 1 µl each of 10 pmol/µl forward and reverse primer , 15.4 µl of sterile Milli-Q water, and 1 µl of DNA template. .. PCR amplification was carried out in an Eppendorf Master Cycler (22331, Eppendorf, Germany) using the following temperature program: initial denaturation (1 min, 94°C) followed by 35 cycles of denaturation (1 min, 94°C), annealing (1 min, 55°C), and elongation (1 min, 72°C) and then final extension (7 min, 72°C).

    Article Title: Association between Three Mutations, F1565C, V1023G and S996P, in the Voltage-Sensitive Sodium Channel Gene and Knockdown Resistance in Aedes aegypti from Yogyakarta, Indonesia
    Article Snippet: .. For site 1565, the 10 μL PCR reaction contained 2 μL of 1 in 10 diluted template DNA, 0.4 μL each of the primers at 10 μM, 1 μL of the ThermoPol reaction buffer (NEB Inc., Ipswich, MA, USA; Cat. No. B9004S), 0.064 μL of dNTP’s at 25 mM (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-39029), 0.4 μL of MgCl2 (50 mM) (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-21047), 0.25 μL of the LightCycler® 480 High Resolution Melting Master (Roche, Mannheim, Germany; Cat. No. 04909631001), 0.01 μL of IMMOLASE™ DNA polymerase (10 u/μL) (Bioline, Alexandria, NSW, Australia; Cat. No. BIO-21047) and 5.476 μL of ddH2 O (Honeywell, Burdick and Jackson; Muskegon, MI, USA; Cat. No. 365-4). .. PCR amplification was carried out using the Roche LightCycler® 480 system (384-well format).

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: .. The 50 µl PCR assay mix contained 32.8 µl of sterile Milli-Q water, 1 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 5 µL of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs), 3 µl each of 10 pmol/µl forward and reverse primer , 0.2 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), and 5 µl of DNA template. .. PCR amplification was carried out using the following temperature program: initial denaturation (5 min, 95°C) followed by 25 cycles of denaturation (45 sec, 94°C), annealing (1 min, at primer-specific temperature [ ]), and elongation (1 min, 72°C) and then final extension (10 min, 72°C).

    Article Title: Exploring protein-DNA interactions in 3D using in situ construction, manipulation, and visualization of individual DNA-dumbbells with optical traps, microfluidics, and fluorescence microscopy
    Article Snippet: .. 5-(3-aminoallyl) dUTP (Fermentas #R0091) Adenosine 5′-O-(3-thiotriphosphate) (ATPγS Calbiotech #119120) ATTO565 NHS-ester (ATTO-TEC GmbH #AD 565-31) Avidin agarose (Thermo Scientific #20219) Biotin-11-dGTP (PerkinElmer #NEL541) Bovine serum albumin (BSA, Sigma-Aldrich #A-9647) Deoxyribonucleoside triphosphates (dNTPs: Invitrogen dATP (#55082), TTP (#55085), dCTP (#55083) and dGTP (#55084) for PCR) Dithiothreitol (DTT Fisher Scientific #BP172-25) CAUTION causes eye and skin irritation; handle wearing goggles, lab coat and gloves Ethanol (EtOH Gold Shield Chemical Company #43196-117) CAUTION flammable; avoid open flames Ethylenediaminetetraacetic acid (EDTA, J. T. Baker #8993-01) Klenow Fragment DNA polymerase I (NEB #M0212S) Magnesium acetate (Mg(OAc)2 J. T. Baker #2424-01) Magnesium chloride (MgCl2 ) Methanol (MeOH Fisher Scientific #A412-4) CAUTION flammable; avoid open flames NEB buffer #2 (NEB buffer supplied with Klenow Fragment DNA polymerase I NEB #B7002S) Phage λ DNA (NEB #N3013S) Potassium hydroxide (KOH Sigma-Aldrich #221473-1KG) CAUTION corrosive; handle wearing goggles, lab coat and gloves Primers for polymerase chain reaction (PCR) to yield a 430 bp product identical to λ DNA between base pairs 23,788 and 24,217: forward primer 5′-biotin-ACTGTTCTTGCGGTTTGGAGG-3′ reverse primer 5′-CTATCGGAAGTTCACCAGCCAG-3′ (can be purchased from any high quality source such as Sigma, Integrated DNA Technologies, or Invitrogen) Sodium bicarbonate (NaHCO3 J. T. Baker #3506-05) Sodium chloride (NaCl) Sodium hydroxide (NaOH) Streptavidin-coated polystyrene beads, 1 μm (Bangs Laboratories #CP01N/10021) Sucrose (Sigma-Aldrich #S7903-5KG) ThermoPol buffer (NEB buffer supplied with VentR ® (exo− ) DNA polymerase NEB #B9004S) Tris acetate (TrisOAc TRIZMA base Sigma-Aldrich #T-1503 + Acetic acid EMD #AX0073-9) CAUTION Acetic acid is corrosive; handle wearing goggles, lab coat and gloves in ventilated hood Water, ultrapure Type 1 (Nanopure (Barnstead) or Milli-Q (Millipore)) VentR ® (exo− ) DNA Polymerase (NEB #M0257) YOYO-1 (Invitrogen #Y3601) .. Abrasive blasting cabinet (Harbor Freight #42202) Computer with design software such as CorelDraw (Corel Corporation) or Illustrator (Adobe Systems Incorporated) Cover glass (Corning No. 1, 24×60 mm #2955-246) Dremel® rotary tool with a diamond coated bit (Dremel #7134) Epoxy, 5 minute (Devcon #14210) Gastight syringes 1000 μl (×4) and 50 μl (×1) (Hamilton #1001 and # 1705) Glass Microscope slides (Fisher Scientific 25×75×1 mm #12-550-A3) Heat block or water bath for maintaining temperature for various reactions High-pressure mercury plasma arc-discharge lamp for curing the optical adhesive (Zeiss 100 watt HBO lamp).

    Article Title: Reasons for the Invasive Success of a Guppy (Poecilia reticulata) Population in Trinidad
    Article Snippet: .. For DNA amplification the following PCR protocol was used: 2.5 µl [25 ng/µl] template, 4.4 µl H2 O, 1 µl PCR buffer [10× Thermobuffer (NEB B9004S)], 1 µl dNTPs [2 mM], 0.1 µl Taq polymerase [5000 U/m (NEB M0267L)], 0.5 µl Fw-primer and 0.5 µl Rev-primer [both 10 pmol/µl]. .. All PCR amplifications run in Peltier Thermal Cyclers pTC-200 from Bio-Rad under the following conditions: 96°C for 3 min, 40 cycles of 96°C for 30 sec., 56°C for 30 sec., 68°C for 30 sec.; 68°C for 5 min.

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: .. The 25 µl reaction mixture contained 2.5 µl of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs, Hertfordshire, UK), 4 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 0.1 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), 1 µl each of 10 pmol/µl forward and reverse primer ( ), 15.4 µl of sterile Milli-Q water, and 1 µl of DNA template. .. PCR amplification was carried out in an Eppendorf Master Cycler (22331, Eppendorf, Germany) using the following temperature program: initial denaturation (1 min, 94°C) followed by 35 cycles of denaturation (1 min, 94°C), annealing (1 min, 55°C), and elongation (1 min, 72°C) and then final extension (7 min, 72°C).

    Article Title: Metabolomic Profiles of a Midge (Procladius villosimanus, Kieffer) Are Associated with Sediment Contamination in Urban Wetlands
    Article Snippet: .. Each PCR reaction was 25 μL and contained the following components: 5 μL Chelex extracted DNA, 2.5 μL ThermoPol 10× buffer (New England Biolabs Ipswich, United States (NEB) Cat. No. B9004S), 2 min μL dNTP (25 mM), 0.2 μL Taq DNA polymerase (NEB Cat. No. M0273S), 1.25 μL each LCO1490 and HC02198 primers (10 μM each) and 12.8 μL of double deionized water. .. The qPCR program was: 3 min at 95 °C, followed by 35 cycles of 1 min at 95 °C, 1 min at 40 °C and 1 min 30 s at 72 °C, followed by a final extension step for 5 min at 72 °C.

    Article Title: A DNA nanoscope via auto-cycling proximity recording
    Article Snippet: After 30 min of incubation, unbound origami and extra staple strands were removed by washing three times with 60 μl of fresh TAE/Mg buffer (40 mM Tris acetate, 1 mM EDTA buffer supplemented with 12.5 mM magnesium acetate) and three times with 60 μl of 1× ThermoPol buffer (NEB, Cat. No. B9004S, 10× ; 1× contains 20 mM Tris-HCl, 10 mM (NH4 )2 SO4 , 10 mM KCl, 2 mM MgSO4 , 0.1% Triton X-100). .. This minimizes any false-positive PCR amplification by the recording primers.

    Article Title: Phenotypic and genotypic characteristics of Trueperellapyogenes isolated from ruminants
    Article Snippet: .. The pld -negative isolates were examined for 8 known and putative virulence genes, utilizing previously developed PCR protocols and primers., The PCR program was performed as follows : denaturation at 95°C for 4 min; 35 cycles of 94°C for 1 min, annealing for 30 s at different temperatures (60°C for nanH -, nanP -, plo -, cbpA -, and fimC -specific PCRs; and 57°C for fimA - and fimG -specific PCRs), , 72°C for 3 min; and a final extension at 72°C for 7 min. All amplifications were carried out in 50 µL of the following reaction mixture: 10 pmol of each primer (0.5 µL each), 10 mM of each dNTP (N0447S, New England BioLabs, Ipswich, MA), 1× Taq polymerase buffer (B9004S, New England BioLabs), 1 U of Taq DNA polymerase (M0273L, New England BioLabs), and ~50 ng of genomic DNA. .. The PCR products were separated by electrophoresis through a 2% agarose gel in Tris–acetate–EDTA buffer (40 mM Tris, 20 mM acetic acid, 1 mM EDTA; Thermo Fisher Scientific, Lenexa, KS), stained with ethidium bromide (MilliporeSigma), and visualized using an Alpha Imager HP (Alpha-Innotech, San Leandro, CA).

    Real-time Polymerase Chain Reaction:

    Article Title: Metabolomic Profiles of a Midge (Procladius villosimanus, Kieffer) Are Associated with Sediment Contamination in Urban Wetlands
    Article Snippet: Each PCR reaction was 25 μL and contained the following components: 5 μL Chelex extracted DNA, 2.5 μL ThermoPol 10× buffer (New England Biolabs Ipswich, United States (NEB) Cat. No. B9004S), 2 min μL dNTP (25 mM), 0.2 μL Taq DNA polymerase (NEB Cat. No. M0273S), 1.25 μL each LCO1490 and HC02198 primers (10 μM each) and 12.8 μL of double deionized water. .. The qPCR program was: 3 min at 95 °C, followed by 35 cycles of 1 min at 95 °C, 1 min at 40 °C and 1 min 30 s at 72 °C, followed by a final extension step for 5 min at 72 °C.

    Avidin-Biotin Assay:

    Article Title: Exploring protein-DNA interactions in 3D using in situ construction, manipulation, and visualization of individual DNA-dumbbells with optical traps, microfluidics, and fluorescence microscopy
    Article Snippet: .. 5-(3-aminoallyl) dUTP (Fermentas #R0091) Adenosine 5′-O-(3-thiotriphosphate) (ATPγS Calbiotech #119120) ATTO565 NHS-ester (ATTO-TEC GmbH #AD 565-31) Avidin agarose (Thermo Scientific #20219) Biotin-11-dGTP (PerkinElmer #NEL541) Bovine serum albumin (BSA, Sigma-Aldrich #A-9647) Deoxyribonucleoside triphosphates (dNTPs: Invitrogen dATP (#55082), TTP (#55085), dCTP (#55083) and dGTP (#55084) for PCR) Dithiothreitol (DTT Fisher Scientific #BP172-25) CAUTION causes eye and skin irritation; handle wearing goggles, lab coat and gloves Ethanol (EtOH Gold Shield Chemical Company #43196-117) CAUTION flammable; avoid open flames Ethylenediaminetetraacetic acid (EDTA, J. T. Baker #8993-01) Klenow Fragment DNA polymerase I (NEB #M0212S) Magnesium acetate (Mg(OAc)2 J. T. Baker #2424-01) Magnesium chloride (MgCl2 ) Methanol (MeOH Fisher Scientific #A412-4) CAUTION flammable; avoid open flames NEB buffer #2 (NEB buffer supplied with Klenow Fragment DNA polymerase I NEB #B7002S) Phage λ DNA (NEB #N3013S) Potassium hydroxide (KOH Sigma-Aldrich #221473-1KG) CAUTION corrosive; handle wearing goggles, lab coat and gloves Primers for polymerase chain reaction (PCR) to yield a 430 bp product identical to λ DNA between base pairs 23,788 and 24,217: forward primer 5′-biotin-ACTGTTCTTGCGGTTTGGAGG-3′ reverse primer 5′-CTATCGGAAGTTCACCAGCCAG-3′ (can be purchased from any high quality source such as Sigma, Integrated DNA Technologies, or Invitrogen) Sodium bicarbonate (NaHCO3 J. T. Baker #3506-05) Sodium chloride (NaCl) Sodium hydroxide (NaOH) Streptavidin-coated polystyrene beads, 1 μm (Bangs Laboratories #CP01N/10021) Sucrose (Sigma-Aldrich #S7903-5KG) ThermoPol buffer (NEB buffer supplied with VentR ® (exo− ) DNA polymerase NEB #B9004S) Tris acetate (TrisOAc TRIZMA base Sigma-Aldrich #T-1503 + Acetic acid EMD #AX0073-9) CAUTION Acetic acid is corrosive; handle wearing goggles, lab coat and gloves in ventilated hood Water, ultrapure Type 1 (Nanopure (Barnstead) or Milli-Q (Millipore)) VentR ® (exo− ) DNA Polymerase (NEB #M0257) YOYO-1 (Invitrogen #Y3601) .. Abrasive blasting cabinet (Harbor Freight #42202) Computer with design software such as CorelDraw (Corel Corporation) or Illustrator (Adobe Systems Incorporated) Cover glass (Corning No. 1, 24×60 mm #2955-246) Dremel® rotary tool with a diamond coated bit (Dremel #7134) Epoxy, 5 minute (Devcon #14210) Gastight syringes 1000 μl (×4) and 50 μl (×1) (Hamilton #1001 and # 1705) Glass Microscope slides (Fisher Scientific 25×75×1 mm #12-550-A3) Heat block or water bath for maintaining temperature for various reactions High-pressure mercury plasma arc-discharge lamp for curing the optical adhesive (Zeiss 100 watt HBO lamp).

    Selection:

    Article Title: Single-molecule nascent RNA sequencing reveals regulatory domain architecture at promoters and enhancers
    Article Snippet: Between adapter ligations, cap state selection reactions were performed. .. 5’ cap was removed with RNA 5’ pyrophosphohydrolase, RppH (NEB, cat. M0356S), using ThermoPol buffer (NEB, cat. B9004S).

    Agarose Gel Electrophoresis:

    Article Title: Phenotypic and genotypic characteristics of Trueperellapyogenes isolated from ruminants
    Article Snippet: The pld -negative isolates were examined for 8 known and putative virulence genes, utilizing previously developed PCR protocols and primers., The PCR program was performed as follows : denaturation at 95°C for 4 min; 35 cycles of 94°C for 1 min, annealing for 30 s at different temperatures (60°C for nanH -, nanP -, plo -, cbpA -, and fimC -specific PCRs; and 57°C for fimA - and fimG -specific PCRs), , 72°C for 3 min; and a final extension at 72°C for 7 min. All amplifications were carried out in 50 µL of the following reaction mixture: 10 pmol of each primer (0.5 µL each), 10 mM of each dNTP (N0447S, New England BioLabs, Ipswich, MA), 1× Taq polymerase buffer (B9004S, New England BioLabs), 1 U of Taq DNA polymerase (M0273L, New England BioLabs), and ~50 ng of genomic DNA. .. The PCR products were separated by electrophoresis through a 2% agarose gel in Tris–acetate–EDTA buffer (40 mM Tris, 20 mM acetic acid, 1 mM EDTA; Thermo Fisher Scientific, Lenexa, KS), stained with ethidium bromide (MilliporeSigma), and visualized using an Alpha Imager HP (Alpha-Innotech, San Leandro, CA).

    Ethanol Precipitation:

    Article Title: Single-molecule nascent RNA sequencing reveals regulatory domain architecture at promoters and enhancers
    Article Snippet: All steps were carried out following the manufacturer’s protocol, with phenol:chloroform extraction and ethanol precipitation between steps. .. 5’ cap was removed with RNA 5’ pyrophosphohydrolase, RppH (NEB, cat. M0356S), using ThermoPol buffer (NEB, cat. B9004S).

    Produced:

    Article Title: A DNA nanoscope via auto-cycling proximity recording
    Article Snippet: After 30 min of incubation, unbound origami and extra staple strands were removed by washing three times with 60 μl of fresh TAE/Mg buffer (40 mM Tris acetate, 1 mM EDTA buffer supplemented with 12.5 mM magnesium acetate) and three times with 60 μl of 1× ThermoPol buffer (NEB, Cat. No. B9004S, 10× ; 1× contains 20 mM Tris-HCl, 10 mM (NH4 )2 SO4 , 10 mM KCl, 2 mM MgSO4 , 0.1% Triton X-100). .. After the recording reaction, the supernatant solution containing produced records was collected and the polymerase was heat inactivated by incubating the solution at 80 °C for 20 min. For samples used in the geometry studies (three-point and hexagonal grid patterns) and the state change study, before quenching the reaction, extra recording primers contained in the product solution were removed by mixing the solution with Exonuclease I (NEB, Cat. No. M0293S) at 9:1 volume ratio and incubating for 20 min at 37 °C.

    Concentration Assay:

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: The MIC was identified as the lowest antibiotic concentration at which no growth (turbidity) was observed. .. The 25 µl reaction mixture contained 2.5 µl of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs, Hertfordshire, UK), 4 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 0.1 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), 1 µl each of 10 pmol/µl forward and reverse primer , 15.4 µl of sterile Milli-Q water, and 1 µl of DNA template.

    Article Title: Efficient and Specific Detection of Salmonella in Food Samples Using a stn-Based Loop-Mediated Isothermal Amplification Method
    Article Snippet: .. LAMP Reaction and LAMP Product Detection The LAMP reaction was performed in a total volume of 25 μ L containing the following components (final concentration): 1.6 μ M each of FIP and BIP primers, 0.2 μ M each of F3 and B3 primers, 0.8 μ M each of LF and LB primers (in the same LAMP reaction), 1.6 mM of deoxyribonucleotide triphosphate mixture (dNTPs), 1 M betaine (Sigma, B2629, St. Louis, USA), 6 mM MgSO4 , 1x thermopol buffer (New England Biolabs, B9004S, Beverly, USA), 1 μ L (8 U) of B st DNA polymerase large fragment (New England Biolabs, M0275S, Beverly, USA), and 5 μ L of DNA template solution. ..

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: The MIC was identified as the lowest antibiotic concentration at which no growth (turbidity) was observed. .. The 25 µl reaction mixture contained 2.5 µl of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs, Hertfordshire, UK), 4 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 0.1 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), 1 µl each of 10 pmol/µl forward and reverse primer ( ), 15.4 µl of sterile Milli-Q water, and 1 µl of DNA template.

    Article Title: A DNA nanoscope via auto-cycling proximity recording
    Article Snippet: After washing the chamber three times with 60 μl of TAE/Mg buffer by adding the buffer to one reservoir (inlet) and subsequently taking out the same volume from the other side (outlet), a 30 μl solution containing origami at 50 pM concentration was introduced to the chamber. (In the first washing round, ~30 μl of buffer occupies the chamber and only ~30 μl of extra buffer comes out.) .. After 30 min of incubation, unbound origami and extra staple strands were removed by washing three times with 60 μl of fresh TAE/Mg buffer (40 mM Tris acetate, 1 mM EDTA buffer supplemented with 12.5 mM magnesium acetate) and three times with 60 μl of 1× ThermoPol buffer (NEB, Cat. No. B9004S, 10× ; 1× contains 20 mM Tris-HCl, 10 mM (NH4 )2 SO4 , 10 mM KCl, 2 mM MgSO4 , 0.1% Triton X-100).

    Marker:

    Article Title: Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes
    Article Snippet: U1/5.8s-rRNA and U4 snRNAs were purified by cutting out the 164nt and 141nt bands respectively, using the low-range ssRNA ladder as a size marker (NEB N0364). snRNAs were gel eluted in elution buffer [0.4 M NaCl, 10 mM Tris pH 7.5, 1 mM EDTA pH 8] at 16 °C overnight with shaking at 2000 rpm. .. Up to 100 ng of each snRNA was decapped in a 10 µl reaction with 1x ThermoPol buffer (NEB B9004S) and 5U RppH (NEB M0356) for 2 hr at 37 °C.

    Staining:

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: Bifidobacterium isolates were phenotypically characterized by Gram staining and catalase reaction. .. The 25 µl reaction mixture contained 2.5 µl of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs, Hertfordshire, UK), 4 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 0.1 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), 1 µl each of 10 pmol/µl forward and reverse primer , 15.4 µl of sterile Milli-Q water, and 1 µl of DNA template.

    Article Title: Atlas of quantitative single-base-resolution N6-methyl-adenine methylomes
    Article Snippet: snRNA isolation and nucleoside UHPLC-MS/MS Nuclear-enriched RNA was resolved on a 6% TBE-urea gel then stained with SYBR-gold (Invitrogen S11494). .. Up to 100 ng of each snRNA was decapped in a 10 µl reaction with 1x ThermoPol buffer (NEB B9004S) and 5U RppH (NEB M0356) for 2 hr at 37 °C.

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: The 50 µl PCR assay mix contained 32.8 µl of sterile Milli-Q water, 1 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 5 µL of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs), 3 µl each of 10 pmol/µl forward and reverse primer , 0.2 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), and 5 µl of DNA template. .. All PCR amplicons were visualized by electrophoresis on 1% (1.2% for ITS-PCR) agarose gels containing 2 µl GelRed stain (41003, Biotium, Fremont, CA, USA); wells were loaded with 10 µl of PCR product + 2 µl of loading dye (R0611, Thermo Fisher Scientific, Loughborough, UK).

    Article Title: Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress
    Article Snippet: Bifidobacterium isolates were phenotypically characterized by Gram staining and catalase reaction. .. The 25 µl reaction mixture contained 2.5 µl of 10x PCR buffer including 20 mM MgCl2 (B9004S, New England Biolabs, Hertfordshire, UK), 4 µl of 1.25 mM dNTP mix (N0447, New England Biolabs), 0.1 µl of 5U Taq DNA polymerase (M0267X, New England Biolabs), 1 µl each of 10 pmol/µl forward and reverse primer ( ), 15.4 µl of sterile Milli-Q water, and 1 µl of DNA template.

    Article Title: Metabolomic Profiles of a Midge (Procladius villosimanus, Kieffer) Are Associated with Sediment Contamination in Urban Wetlands
    Article Snippet: Each PCR reaction was 25 μL and contained the following components: 5 μL Chelex extracted DNA, 2.5 μL ThermoPol 10× buffer (New England Biolabs Ipswich, United States (NEB) Cat. No. B9004S), 2 min μL dNTP (25 mM), 0.2 μL Taq DNA polymerase (NEB Cat. No. M0273S), 1.25 μL each LCO1490 and HC02198 primers (10 μM each) and 12.8 μL of double deionized water. .. Amplification bands of correct size were confirmed with gel electrophoresis, using 2% agarose gels, stained with sybr safe (Thermo Fisher Scientific Cat No.: S33102).

    Article Title: Phenotypic and genotypic characteristics of Trueperellapyogenes isolated from ruminants
    Article Snippet: The pld -negative isolates were examined for 8 known and putative virulence genes, utilizing previously developed PCR protocols and primers., The PCR program was performed as follows : denaturation at 95°C for 4 min; 35 cycles of 94°C for 1 min, annealing for 30 s at different temperatures (60°C for nanH -, nanP -, plo -, cbpA -, and fimC -specific PCRs; and 57°C for fimA - and fimG -specific PCRs), , 72°C for 3 min; and a final extension at 72°C for 7 min. All amplifications were carried out in 50 µL of the following reaction mixture: 10 pmol of each primer (0.5 µL each), 10 mM of each dNTP (N0447S, New England BioLabs, Ipswich, MA), 1× Taq polymerase buffer (B9004S, New England BioLabs), 1 U of Taq DNA polymerase (M0273L, New England BioLabs), and ~50 ng of genomic DNA. .. The PCR products were separated by electrophoresis through a 2% agarose gel in Tris–acetate–EDTA buffer (40 mM Tris, 20 mM acetic acid, 1 mM EDTA; Thermo Fisher Scientific, Lenexa, KS), stained with ethidium bromide (MilliporeSigma), and visualized using an Alpha Imager HP (Alpha-Innotech, San Leandro, CA).

    Fluorescence In Situ Hybridization:

    Article Title: Reasons for the Invasive Success of a Guppy (Poecilia reticulata) Population in Trinidad
    Article Snippet: In June and July 2010, all fish samples were taken to the Max Planck Institute for Developmental Biology in Tuebingen, Germany, for genetic analysis. .. For DNA amplification the following PCR protocol was used: 2.5 µl [25 ng/µl] template, 4.4 µl H2 O, 1 µl PCR buffer [10× Thermobuffer (NEB B9004S)], 1 µl dNTPs [2 mM], 0.1 µl Taq polymerase [5000 U/m (NEB M0267L)], 0.5 µl Fw-primer and 0.5 µl Rev-primer [both 10 pmol/µl].

    Hood:

    Article Title: Exploring protein-DNA interactions in 3D using in situ construction, manipulation, and visualization of individual DNA-dumbbells with optical traps, microfluidics, and fluorescence microscopy
    Article Snippet: .. 5-(3-aminoallyl) dUTP (Fermentas #R0091) Adenosine 5′-O-(3-thiotriphosphate) (ATPγS Calbiotech #119120) ATTO565 NHS-ester (ATTO-TEC GmbH #AD 565-31) Avidin agarose (Thermo Scientific #20219) Biotin-11-dGTP (PerkinElmer #NEL541) Bovine serum albumin (BSA, Sigma-Aldrich #A-9647) Deoxyribonucleoside triphosphates (dNTPs: Invitrogen dATP (#55082), TTP (#55085), dCTP (#55083) and dGTP (#55084) for PCR) Dithiothreitol (DTT Fisher Scientific #BP172-25) CAUTION causes eye and skin irritation; handle wearing goggles, lab coat and gloves Ethanol (EtOH Gold Shield Chemical Company #43196-117) CAUTION flammable; avoid open flames Ethylenediaminetetraacetic acid (EDTA, J. T. Baker #8993-01) Klenow Fragment DNA polymerase I (NEB #M0212S) Magnesium acetate (Mg(OAc)2 J. T. Baker #2424-01) Magnesium chloride (MgCl2 ) Methanol (MeOH Fisher Scientific #A412-4) CAUTION flammable; avoid open flames NEB buffer #2 (NEB buffer supplied with Klenow Fragment DNA polymerase I NEB #B7002S) Phage λ DNA (NEB #N3013S) Potassium hydroxide (KOH Sigma-Aldrich #221473-1KG) CAUTION corrosive; handle wearing goggles, lab coat and gloves Primers for polymerase chain reaction (PCR) to yield a 430 bp product identical to λ DNA between base pairs 23,788 and 24,217: forward primer 5′-biotin-ACTGTTCTTGCGGTTTGGAGG-3′ reverse primer 5′-CTATCGGAAGTTCACCAGCCAG-3′ (can be purchased from any high quality source such as Sigma, Integrated DNA Technologies, or Invitrogen) Sodium bicarbonate (NaHCO3 J. T. Baker #3506-05) Sodium chloride (NaCl) Sodium hydroxide (NaOH) Streptavidin-coated polystyrene beads, 1 μm (Bangs Laboratories #CP01N/10021) Sucrose (Sigma-Aldrich #S7903-5KG) ThermoPol buffer (NEB buffer supplied with VentR ® (exo− ) DNA polymerase NEB #B9004S) Tris acetate (TrisOAc TRIZMA base Sigma-Aldrich #T-1503 + Acetic acid EMD #AX0073-9) CAUTION Acetic acid is corrosive; handle wearing goggles, lab coat and gloves in ventilated hood Water, ultrapure Type 1 (Nanopure (Barnstead) or Milli-Q (Millipore)) VentR ® (exo− ) DNA Polymerase (NEB #M0257) YOYO-1 (Invitrogen #Y3601) .. Abrasive blasting cabinet (Harbor Freight #42202) Computer with design software such as CorelDraw (Corel Corporation) or Illustrator (Adobe Systems Incorporated) Cover glass (Corning No. 1, 24×60 mm #2955-246) Dremel® rotary tool with a diamond coated bit (Dremel #7134) Epoxy, 5 minute (Devcon #14210) Gastight syringes 1000 μl (×4) and 50 μl (×1) (Hamilton #1001 and # 1705) Glass Microscope slides (Fisher Scientific 25×75×1 mm #12-550-A3) Heat block or water bath for maintaining temperature for various reactions High-pressure mercury plasma arc-discharge lamp for curing the optical adhesive (Zeiss 100 watt HBO lamp).

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  • 90
    New England Biolabs b9004s
    B9004s, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 12 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/b9004s/product/New England Biolabs
    Average 90 stars, based on 12 article reviews
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