nickase  (New England Biolabs)


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    Name:
    Nt BstNBI
    Description:
    Nt BstNBI 5 000 units
    Catalog Number:
    R0607L
    Price:
    290
    Category:
    Restriction Enzymes
    Size:
    5 000 units
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    New England Biolabs nickase
    Nt BstNBI
    Nt BstNBI 5 000 units
    https://www.bioz.com/result/nickase/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nickase - by Bioz Stars, 2021-06
    99/100 stars

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    Related Articles

    SYBR Green Assay:

    Article Title: Sequence dependence of isothermal DNA amplification via EXPAR
    Article Snippet: Corresponding trigger sequences were obtained from Eurofins MWG Operon (Huntsville, AL). .. EXPAR was performed in a 30 µl reaction mixture containing 0.2 units/µl Nt.BstNBI nicking enzyme (New England Biolabs, Ipswich, MA), 0.03 U/µl Bst DNA Polymerase (NEB), 0.24 mM of each dNTP (Fermentas, Glen Burnie, MD), 3 mM MgCl2 (Sigma-Aldrich, St. Louis, MO), 1× Sybr Green I (Invitrogen), 20 mM Tris–HCl pH 7.9, 15 mM ammonium sulfate, 30 mM KCl, 0.005% Triton X-100, and 50 nM EXPAR template oligonucleotide. ..

    Plasmid Preparation:

    Article Title: A Rapid, Simple DNA Mismatch Repair Substrate Construction Method
    Article Snippet: .. Generation of gap DNA For a typical digestion reaction, 400 μg of plasmid DNA were used and 400 units of Nt.BstNBI were added in the reaction containing NEBuffer 3 buffer, and digestion was performed at 55°C for 4–6 h. At least 90% of supercoiled plasmid DNA was transformed into nick DNA. ..

    Transformation Assay:

    Article Title: A Rapid, Simple DNA Mismatch Repair Substrate Construction Method
    Article Snippet: .. Generation of gap DNA For a typical digestion reaction, 400 μg of plasmid DNA were used and 400 units of Nt.BstNBI were added in the reaction containing NEBuffer 3 buffer, and digestion was performed at 55°C for 4–6 h. At least 90% of supercoiled plasmid DNA was transformed into nick DNA. ..

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    New England Biolabs nt bstnbi nease
    Effect of biotin tag on EXPAR. ( A ) Diagram of the experimental setup. ( B ) Determination of Tm of duplexes of let-7a/standard template and let-7a/biotin-template-2 by a StepOneplus Real-Time PCR System (Applied Biosystems, USA) using SYBR Green I as the reporter dye. The biotin-template-2 is a standard template labeled with a biotin at the second base from its 5′ terminus. T m curves were obtained from the derivative of the fluorescence intensity as a function of temperature. The temperature was increased from 45°C to 95°C at a rate of 5°C min –1 . ( C ) Real-time fluorescence curves of EXPAR reactions at 55°C with 0.05 U μl –1 Vent (exo-) DNA polymerase, 0.4 U μl –1 <t>Nt.BstNBI</t> <t>NEase,</t> 6.02 × 10 9 copies (10 fmol) let-7a and 1 μM standard template or biotin-template-1, 2, 6, 10, 14, 18. The biotin-template-1, 2, 6, 10, 14, 18 are standard templates labeled with a biotin at the first, second, sixth, 10th, 14th, 18th base from their 5′ terminus, respectively.
    Nt Bstnbi Nease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nt bstnbi nease/product/New England Biolabs
    Average 99 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    nt bstnbi nease - by Bioz Stars, 2021-06
    99/100 stars
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    Effect of biotin tag on EXPAR. ( A ) Diagram of the experimental setup. ( B ) Determination of Tm of duplexes of let-7a/standard template and let-7a/biotin-template-2 by a StepOneplus Real-Time PCR System (Applied Biosystems, USA) using SYBR Green I as the reporter dye. The biotin-template-2 is a standard template labeled with a biotin at the second base from its 5′ terminus. T m curves were obtained from the derivative of the fluorescence intensity as a function of temperature. The temperature was increased from 45°C to 95°C at a rate of 5°C min –1 . ( C ) Real-time fluorescence curves of EXPAR reactions at 55°C with 0.05 U μl –1 Vent (exo-) DNA polymerase, 0.4 U μl –1 Nt.BstNBI NEase, 6.02 × 10 9 copies (10 fmol) let-7a and 1 μM standard template or biotin-template-1, 2, 6, 10, 14, 18. The biotin-template-1, 2, 6, 10, 14, 18 are standard templates labeled with a biotin at the first, second, sixth, 10th, 14th, 18th base from their 5′ terminus, respectively.

    Journal: Nucleic Acids Research

    Article Title: Asymmetric exponential amplification reaction on a toehold/biotin featured template: an ultrasensitive and specific strategy for isothermal microRNAs analysis

    doi: 10.1093/nar/gkw504

    Figure Lengend Snippet: Effect of biotin tag on EXPAR. ( A ) Diagram of the experimental setup. ( B ) Determination of Tm of duplexes of let-7a/standard template and let-7a/biotin-template-2 by a StepOneplus Real-Time PCR System (Applied Biosystems, USA) using SYBR Green I as the reporter dye. The biotin-template-2 is a standard template labeled with a biotin at the second base from its 5′ terminus. T m curves were obtained from the derivative of the fluorescence intensity as a function of temperature. The temperature was increased from 45°C to 95°C at a rate of 5°C min –1 . ( C ) Real-time fluorescence curves of EXPAR reactions at 55°C with 0.05 U μl –1 Vent (exo-) DNA polymerase, 0.4 U μl –1 Nt.BstNBI NEase, 6.02 × 10 9 copies (10 fmol) let-7a and 1 μM standard template or biotin-template-1, 2, 6, 10, 14, 18. The biotin-template-1, 2, 6, 10, 14, 18 are standard templates labeled with a biotin at the first, second, sixth, 10th, 14th, 18th base from their 5′ terminus, respectively.

    Article Snippet: Vent (exo-) DNA polymerase and Nt.BstNBI NEase were purchased from New England Biolabs (Beijing, China).

    Techniques: Real-time Polymerase Chain Reaction, SYBR Green Assay, Labeling, Fluorescence

    Tetrastable system built from two cross-inhibitory bistable switches. (a) Schematic of the tetrastable DNA circuit. Two microRNA-sensing circuits (cT, aT, pT, and rT) are interconnected by kT αkβ and βkα, which repress unwanted cross-activation. (b) Detailed mechanism of the five kinds of templates (pol. = Vent(exo-), nick. 1 = Nt.BstNBI, nick. 2 = Nb.BsmI, RE = BsmI, and exo. = ttRecJ). cTs convert the complementary microRNA target to a signal strand (α or β). Autocataytic templates (aTs) exponentially amplify the signal strands. pTs, by deactivating a fraction of signal strands, suppress background amplification stemming from biochemical noise. Reporting templates (rTs) transduce the molecular signal (α or β) to a detectable fluorescence signal (green = Oregon green fluorophore, red = Atto633 fluorophore). From the α or β strands, killer templates (kTs) produce pTs of the opposite switch, mitigating unspecific cross-talks. All produced strands are continuously degraded by the exonuclease to maintain the system dynamics and avoid system poisoning by the accumulation of DNA strands. Only one half of the tetrastable circuit is represented here, the second half being obtained by substituting α by β and conversely.

    Journal: ACS Sensors

    Article Title: Multiplex Digital MicroRNA Detection Using Cross-Inhibitory DNA Circuits

    doi: 10.1021/acssensors.0c00593

    Figure Lengend Snippet: Tetrastable system built from two cross-inhibitory bistable switches. (a) Schematic of the tetrastable DNA circuit. Two microRNA-sensing circuits (cT, aT, pT, and rT) are interconnected by kT αkβ and βkα, which repress unwanted cross-activation. (b) Detailed mechanism of the five kinds of templates (pol. = Vent(exo-), nick. 1 = Nt.BstNBI, nick. 2 = Nb.BsmI, RE = BsmI, and exo. = ttRecJ). cTs convert the complementary microRNA target to a signal strand (α or β). Autocataytic templates (aTs) exponentially amplify the signal strands. pTs, by deactivating a fraction of signal strands, suppress background amplification stemming from biochemical noise. Reporting templates (rTs) transduce the molecular signal (α or β) to a detectable fluorescence signal (green = Oregon green fluorophore, red = Atto633 fluorophore). From the α or β strands, killer templates (kTs) produce pTs of the opposite switch, mitigating unspecific cross-talks. All produced strands are continuously degraded by the exonuclease to maintain the system dynamics and avoid system poisoning by the accumulation of DNA strands. Only one half of the tetrastable circuit is represented here, the second half being obtained by substituting α by β and conversely.

    Article Snippet: The nicking enzymes Nb.BsmI and Nt.bstNBI, the restriction enzyme BsmI, the DNA polymerase Vent(exo-), BSA, and dNTP were obtained from New England Biolabs (NEB).

    Techniques: Activation Assay, Amplification, Fluorescence, Produced

    Illustration of the whole procedure of this new method . (1) the original pWDAH1A/SH1B plasmid; (2) Nt. BstNBI digestion to produce two nicks followed by addition of 20× biotinylated supplementary oligo; (3) two rounds of treatment with streptavidin beads and column to remove the biotinylated oligo to generate gap DNA; (4) the mismatch-containing DNA oligo added to anneal with the gap DNA, followed by a ligation reaction; (5) CsCl density ultracentrifuge, DNA recovery, and nick generation using Nt.BbvCI or Nb.BbvCI; (6) mismatch-containing DNA substrate (G/T mismatch or G/IU).

    Journal: Frontiers in Oncology

    Article Title: A Rapid, Simple DNA Mismatch Repair Substrate Construction Method

    doi: 10.3389/fonc.2011.00008

    Figure Lengend Snippet: Illustration of the whole procedure of this new method . (1) the original pWDAH1A/SH1B plasmid; (2) Nt. BstNBI digestion to produce two nicks followed by addition of 20× biotinylated supplementary oligo; (3) two rounds of treatment with streptavidin beads and column to remove the biotinylated oligo to generate gap DNA; (4) the mismatch-containing DNA oligo added to anneal with the gap DNA, followed by a ligation reaction; (5) CsCl density ultracentrifuge, DNA recovery, and nick generation using Nt.BbvCI or Nb.BbvCI; (6) mismatch-containing DNA substrate (G/T mismatch or G/IU).

    Article Snippet: Generation of gap DNA For a typical digestion reaction, 400 μg of plasmid DNA were used and 400 units of Nt.BstNBI were added in the reaction containing NEBuffer 3 buffer, and digestion was performed at 55°C for 4–6 h. At least 90% of supercoiled plasmid DNA was transformed into nick DNA.

    Techniques: Plasmid Preparation, Ligation

    Identification of gap DNA . Lane 1: 200 ng of pWDAH1A plasmid; Lane 2: Nt. BstNBI-digested pWDAH1A plasmid (Nick DNA), 200 ng; Lane 3: Nt.BstNBI-digested pWDAH1A plasmid + biotinylated Rem-seq oligo; Lane 4: flow-through of mixture of lane 3; Lane 5: gap DNA, 200 ng; Lane 6: NheI-digested pWDAH1A plasmid DNA (linear DNA); Lane 7: NheI digestion of 200 ng gap DNA; Lane 8: ligation of gap DNA. Two hundred nanograms of DNA loaded each lane.

    Journal: Frontiers in Oncology

    Article Title: A Rapid, Simple DNA Mismatch Repair Substrate Construction Method

    doi: 10.3389/fonc.2011.00008

    Figure Lengend Snippet: Identification of gap DNA . Lane 1: 200 ng of pWDAH1A plasmid; Lane 2: Nt. BstNBI-digested pWDAH1A plasmid (Nick DNA), 200 ng; Lane 3: Nt.BstNBI-digested pWDAH1A plasmid + biotinylated Rem-seq oligo; Lane 4: flow-through of mixture of lane 3; Lane 5: gap DNA, 200 ng; Lane 6: NheI-digested pWDAH1A plasmid DNA (linear DNA); Lane 7: NheI digestion of 200 ng gap DNA; Lane 8: ligation of gap DNA. Two hundred nanograms of DNA loaded each lane.

    Article Snippet: Generation of gap DNA For a typical digestion reaction, 400 μg of plasmid DNA were used and 400 units of Nt.BstNBI were added in the reaction containing NEBuffer 3 buffer, and digestion was performed at 55°C for 4–6 h. At least 90% of supercoiled plasmid DNA was transformed into nick DNA.

    Techniques: Plasmid Preparation, Flow Cytometry, Ligation

    Confirmation of RPA, GQ-catalysed TMB oxidation and LSDA reactions. a) RPA with SC1 forward and reverse primers containing Nt.AlwI or Nt.BstNBI recognition site . Each reaction was performed using genomic S. cerevisiae BY4741 DNA as a target sequence. The target sequence is absent in the negative control. The positive control was performed with the primers and target templates provided by the TwistAmp Basic kit (TwistDx). b) Average TMB oxidation rate of different GQ DNAzyme sequences. Here, the catalytic activities of EAD2+3’A, BBa_K1614007, and BBa_K1614007+3’A GQ DNAzymes (Table S2) in pH 6.0 phosphate buffer were compared. The concentration of DNAzyme was kept at 1 μM in all measurements. EAD2+3’A was identified as the most potent DNAzyme in catalysing TMB oxidation. The error bars represented the standard deviation of three replicates. c) TMB oxidation by EAD2+3’A DNAzyme. Kinetic parameters of the DNAzyme were measured based on its ability to catalyse TMB oxidation reaction at different TMB concentrations. In the figure, data points represent initial oxidation rate measured from each experimental replicate while the curve represents model-predicted kinetics at each given TMB concentration. Rate kinetics of EAD2+3’A were assumed to follow Michaelis-Menten kinetics. The initial rate of each individual replicates was calculated based on differences in oxidized TMB absorbance value at 650 nm for the first minute of the observation. The resulting model could sufficiently describe each individual replicate measurement (Fig. S1). d) GQ DNAzyme production using LSDA reaction. LSDA was performed using different nickases. Here we identified Nt.BstNBI as the most potent GQ-producer. Synthetic (pure) oligonucleotides (Table S3) containing the targeted S. cerevisiae genome, nickase site and EAD2+3’A DNAzyme sequences were used as template for the LSDA reaction. The figure shows the average of two replicates.

    Journal: bioRxiv

    Article Title: Rapidemic, a versatile and label-free DNAzyme-based platform for visual nucleic acid detection

    doi: 10.1101/2020.10.14.337808

    Figure Lengend Snippet: Confirmation of RPA, GQ-catalysed TMB oxidation and LSDA reactions. a) RPA with SC1 forward and reverse primers containing Nt.AlwI or Nt.BstNBI recognition site . Each reaction was performed using genomic S. cerevisiae BY4741 DNA as a target sequence. The target sequence is absent in the negative control. The positive control was performed with the primers and target templates provided by the TwistAmp Basic kit (TwistDx). b) Average TMB oxidation rate of different GQ DNAzyme sequences. Here, the catalytic activities of EAD2+3’A, BBa_K1614007, and BBa_K1614007+3’A GQ DNAzymes (Table S2) in pH 6.0 phosphate buffer were compared. The concentration of DNAzyme was kept at 1 μM in all measurements. EAD2+3’A was identified as the most potent DNAzyme in catalysing TMB oxidation. The error bars represented the standard deviation of three replicates. c) TMB oxidation by EAD2+3’A DNAzyme. Kinetic parameters of the DNAzyme were measured based on its ability to catalyse TMB oxidation reaction at different TMB concentrations. In the figure, data points represent initial oxidation rate measured from each experimental replicate while the curve represents model-predicted kinetics at each given TMB concentration. Rate kinetics of EAD2+3’A were assumed to follow Michaelis-Menten kinetics. The initial rate of each individual replicates was calculated based on differences in oxidized TMB absorbance value at 650 nm for the first minute of the observation. The resulting model could sufficiently describe each individual replicate measurement (Fig. S1). d) GQ DNAzyme production using LSDA reaction. LSDA was performed using different nickases. Here we identified Nt.BstNBI as the most potent GQ-producer. Synthetic (pure) oligonucleotides (Table S3) containing the targeted S. cerevisiae genome, nickase site and EAD2+3’A DNAzyme sequences were used as template for the LSDA reaction. The figure shows the average of two replicates.

    Article Snippet: Nicking endonucleases, including Nt.BstNBI, Nt.AlwI and Nt.BsmAI, and Bst 2.0 DNA Polymerase were acquired from New England Biolabs (NEB).

    Techniques: Recombinase Polymerase Amplification, Sequencing, Negative Control, Positive Control, Concentration Assay, Standard Deviation