endoviii  (New England Biolabs)


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  • 94
    Name:
    Endonuclease VIII
    Description:
    Endonuclease VIII 5 000 units
    Catalog Number:
    m0299l
    Price:
    306
    Size:
    5 000 units
    Category:
    Other Endonucleases
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    Structured Review

    New England Biolabs endoviii
    Endonuclease VIII
    Endonuclease VIII 5 000 units
    https://www.bioz.com/result/endoviii/product/New England Biolabs
    Average 94 stars, based on 43 article reviews
    Price from $9.99 to $1999.99
    endoviii - by Bioz Stars, 2021-01
    94/100 stars

    Images

    1) Product Images from "USER(TM) friendly DNA engineering and cloning method by uracil excision"

    Article Title: USER(TM) friendly DNA engineering and cloning method by uracil excision

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkm041

    USER enzyme activity assay. A 34-mer oligonucleotide duplex (10 pmol) containing a single dU paired with a deoxyadenine ( Table 1 ) was incubated with a series of EndoVIII and UDG enzyme mixtures for 15 min at 37°C in a 10 μl of T4 DNA ligase reaction buffer (50 mM Tris-HCl pH 7.5, 10 mM MgCl 2 , 10 mM DTT, 1 mM ATP, 20 μg/ml BSA). The reactions were quenched by the addition of 10 μl of 95% formamide, 0.1% xylene cyanol, 0.1% bromophenol blue, 10 mM EDTA, pH 11, and the reaction products were analyzedon a 15% TBE-Urea denaturing gel. S, 34-nt oligonucleotide substrate. P1 and P2, 15 nt and 18 nt cleavage products, respectively. Two product bands of differing size result from the fact that the uracil is not in the centre of the substrate. Lane 1—no enzyme added. Lane 2—reaction contains 0.2 units of UDG. Lane 3—reaction contains 256 ng of EndoVIII. Lanes 4–10, reaction contains 0.2 units of UDG and the amount of EndoVIII shown above the respective lanes.
    Figure Legend Snippet: USER enzyme activity assay. A 34-mer oligonucleotide duplex (10 pmol) containing a single dU paired with a deoxyadenine ( Table 1 ) was incubated with a series of EndoVIII and UDG enzyme mixtures for 15 min at 37°C in a 10 μl of T4 DNA ligase reaction buffer (50 mM Tris-HCl pH 7.5, 10 mM MgCl 2 , 10 mM DTT, 1 mM ATP, 20 μg/ml BSA). The reactions were quenched by the addition of 10 μl of 95% formamide, 0.1% xylene cyanol, 0.1% bromophenol blue, 10 mM EDTA, pH 11, and the reaction products were analyzedon a 15% TBE-Urea denaturing gel. S, 34-nt oligonucleotide substrate. P1 and P2, 15 nt and 18 nt cleavage products, respectively. Two product bands of differing size result from the fact that the uracil is not in the centre of the substrate. Lane 1—no enzyme added. Lane 2—reaction contains 0.2 units of UDG. Lane 3—reaction contains 256 ng of EndoVIII. Lanes 4–10, reaction contains 0.2 units of UDG and the amount of EndoVIII shown above the respective lanes.

    Techniques Used: Enzyme Activity Assay, Incubation

    2) Product Images from "USER(TM) friendly DNA engineering and cloning method by uracil excision"

    Article Title: USER(TM) friendly DNA engineering and cloning method by uracil excision

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkm041

    USER enzyme activity assay. A 34-mer oligonucleotide duplex (10 pmol) containing a single dU paired with a deoxyadenine ( Table 1 ) was incubated with a series of EndoVIII and UDG enzyme mixtures for 15 min at 37°C in a 10 μl of T4 DNA ligase reaction buffer (50 mM Tris-HCl pH 7.5, 10 mM MgCl 2 , 10 mM DTT, 1 mM ATP, 20 μg/ml BSA). The reactions were quenched by the addition of 10 μl of 95% formamide, 0.1% xylene cyanol, 0.1% bromophenol blue, 10 mM EDTA, pH 11, and the reaction products were analyzedon a 15% TBE-Urea denaturing gel. S, 34-nt oligonucleotide substrate. P1 and P2, 15 nt and 18 nt cleavage products, respectively. Two product bands of differing size result from the fact that the uracil is not in the centre of the substrate. Lane 1—no enzyme added. Lane 2—reaction contains 0.2 units of UDG. Lane 3—reaction contains 256 ng of EndoVIII. Lanes 4–10, reaction contains 0.2 units of UDG and the amount of EndoVIII shown above the respective lanes.
    Figure Legend Snippet: USER enzyme activity assay. A 34-mer oligonucleotide duplex (10 pmol) containing a single dU paired with a deoxyadenine ( Table 1 ) was incubated with a series of EndoVIII and UDG enzyme mixtures for 15 min at 37°C in a 10 μl of T4 DNA ligase reaction buffer (50 mM Tris-HCl pH 7.5, 10 mM MgCl 2 , 10 mM DTT, 1 mM ATP, 20 μg/ml BSA). The reactions were quenched by the addition of 10 μl of 95% formamide, 0.1% xylene cyanol, 0.1% bromophenol blue, 10 mM EDTA, pH 11, and the reaction products were analyzedon a 15% TBE-Urea denaturing gel. S, 34-nt oligonucleotide substrate. P1 and P2, 15 nt and 18 nt cleavage products, respectively. Two product bands of differing size result from the fact that the uracil is not in the centre of the substrate. Lane 1—no enzyme added. Lane 2—reaction contains 0.2 units of UDG. Lane 3—reaction contains 256 ng of EndoVIII. Lanes 4–10, reaction contains 0.2 units of UDG and the amount of EndoVIII shown above the respective lanes.

    Techniques Used: Enzyme Activity Assay, Incubation

    Related Articles

    Amplification:

    Article Title: Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
    Article Snippet: .. Libraries were built as above, except a DNA repair step in which UDG and endonuclease VIII or USER enzyme (NEB) treatment was included in order to remove deaminated cytosines [ ]. qPCR was performed in order to quantify the number of molecules and the optimal number of PCR cycles prior to amplification for each DNA library. .. Furthermore, this step included extraction blanks, library blanks, and amplification blanks to monitor potential contamination.

    Ligation:

    Article Title: Telomere Trimming and DNA Damage as Signatures of High Risk Neuroblastoma
    Article Snippet: .. In some of STELA assays, 50 ng of genomic DNA was digested with 5 U of Endonuclease VIII (NEB) and 4 U of Fpg (NEB) in 1× CutSmart buffer (NEB) at 37 °C for 2 h. Both glycosylases were inactivated at 75 °C for 20 min. Digested DNAs were applied to the ligation reaction for STELA analysis. .. In-Gel Hybridization Analysis of ssDNA on Telomere G- and C-Strand The standard in-gel hybridization analysis was performed using a combination of established protocols with minor modification .

    Incubation:

    Article Title: Defective base excision repair in the response to DNA damaging agents in triple negative breast cancer
    Article Snippet: .. After permeabilization, cells were incubated with uracil DNA glycosylase (UDG) to remove uracil (NEB #M0304S), formamidopyrimidine [Fapy]-DNA glycosylase (Fapy-DNA glycosylase NEB #M0240S) to remove Fapy lesions, T4 Pyrimidine dimer glycosylase (T4PDG NEB #M-308S) to remove pyrimidine dimer lesions, endonuclease IV (Endo IV NEB #M0304S) to process oxidative damage, AP sites and modifies 3’ phosphates to 3’ OH, and endonuclease VIII (Endo VIII NEB #M0299S) to remove damaged pyrimidines diluted in 1X Thermpol buffer and incubated at 37 degrees C for 1 hour. .. This leaves gaps to be filled by DNA polymerase I Klenow large fragment (lacking 5’ to 3’ exonuclease activity) incubated with Digoxigenin-11-dUTP, alkali-labile (Dig) (Sigma-Aldrich #DIUTP-RO) at 37 degrees C for 1 hour.

    Article Title: Domain Swapping in Allosteric Modulation of DNA Specificity
    Article Snippet: .. Ten units (1 µl) of EndoVIII DNA glycosylase and 10 units (2 µl) of SMUG1 DNA glycosylase (both enzymes from New England Biolabs) were added to the reaction and incubated for 15 min at 37°C to excise 5 hmU residues from PCR product, and then incubated an additional 15 min at room temperature to allow annealing of complementary extensions. .. Escherichia coli T7 Express Iq competent cells (New England Biolabs) were transformed with 5 µl of the annealing reaction.

    Real-time Polymerase Chain Reaction:

    Article Title: Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
    Article Snippet: .. Libraries were built as above, except a DNA repair step in which UDG and endonuclease VIII or USER enzyme (NEB) treatment was included in order to remove deaminated cytosines [ ]. qPCR was performed in order to quantify the number of molecules and the optimal number of PCR cycles prior to amplification for each DNA library. .. Furthermore, this step included extraction blanks, library blanks, and amplification blanks to monitor potential contamination.

    Concentration Assay:

    Article Title: USER(TM) friendly DNA engineering and cloning method by uracil excision
    Article Snippet: .. In the mixes, the concentration of EndoVIII varied from 4 to 256 ng, while the concentration of UDG was kept constant at 0.2 activity units, which is enough to release 12 pmol of uracil per minute (New England Biolabs). ..

    Generated:

    Article Title: Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone
    Article Snippet: .. Sequencing libraries were generated from each DNA extract following a single-stranded library preparation protocol [ ], which included treatment with uracil-DNA glycosylase (New England Biolabs M0279) and endonuclease VIII (New England Biolabs M0299). .. The Klenow Fragment of DNA polymerase I (Thermo Fisher Scientific EP0051) was used for the fill-in reaction [ ].

    Polymerase Chain Reaction:

    Article Title: Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
    Article Snippet: .. Libraries were built as above, except a DNA repair step in which UDG and endonuclease VIII or USER enzyme (NEB) treatment was included in order to remove deaminated cytosines [ ]. qPCR was performed in order to quantify the number of molecules and the optimal number of PCR cycles prior to amplification for each DNA library. .. Furthermore, this step included extraction blanks, library blanks, and amplification blanks to monitor potential contamination.

    Article Title: Domain Swapping in Allosteric Modulation of DNA Specificity
    Article Snippet: .. Ten units (1 µl) of EndoVIII DNA glycosylase and 10 units (2 µl) of SMUG1 DNA glycosylase (both enzymes from New England Biolabs) were added to the reaction and incubated for 15 min at 37°C to excise 5 hmU residues from PCR product, and then incubated an additional 15 min at room temperature to allow annealing of complementary extensions. .. Escherichia coli T7 Express Iq competent cells (New England Biolabs) were transformed with 5 µl of the annealing reaction.

    Activity Assay:

    Article Title: USER(TM) friendly DNA engineering and cloning method by uracil excision
    Article Snippet: .. In the mixes, the concentration of EndoVIII varied from 4 to 256 ng, while the concentration of UDG was kept constant at 0.2 activity units, which is enough to release 12 pmol of uracil per minute (New England Biolabs). ..

    Sequencing:

    Article Title: Reduction of the contaminant fraction of DNA obtained from an ancient giant panda bone
    Article Snippet: .. Sequencing libraries were generated from each DNA extract following a single-stranded library preparation protocol [ ], which included treatment with uracil-DNA glycosylase (New England Biolabs M0279) and endonuclease VIII (New England Biolabs M0299). .. The Klenow Fragment of DNA polymerase I (Thermo Fisher Scientific EP0051) was used for the fill-in reaction [ ].

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    New England Biolabs endoviii
    USER enzyme activity assay. A 34-mer oligonucleotide duplex (10 pmol) containing a single dU paired with a deoxyadenine ( Table 1 ) was incubated with a series of <t>EndoVIII</t> and UDG enzyme mixtures for 15 min at 37°C in a 10 μl of T4 DNA ligase reaction buffer (50 mM Tris-HCl pH 7.5, 10 mM MgCl 2 , 10 mM DTT, 1 mM ATP, 20 μg/ml BSA). The reactions were quenched by the addition of 10 μl of 95% formamide, 0.1% xylene cyanol, 0.1% bromophenol blue, 10 mM EDTA, pH 11, and the reaction products were analyzedon a 15% TBE-Urea denaturing gel. S, 34-nt oligonucleotide substrate. P1 and P2, 15 nt and 18 nt cleavage products, respectively. Two product bands of differing size result from the fact that the uracil is not in the centre of the substrate. Lane 1—no enzyme added. Lane 2—reaction contains 0.2 units of UDG. Lane 3—reaction contains 256 ng of EndoVIII. Lanes 4–10, reaction contains 0.2 units of UDG and the amount of EndoVIII shown above the respective lanes.
    Endoviii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 8 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/endoviii/product/New England Biolabs
    Average 94 stars, based on 8 article reviews
    Price from $9.99 to $1999.99
    endoviii - by Bioz Stars, 2021-01
    94/100 stars
      Buy from Supplier

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    USER enzyme activity assay. A 34-mer oligonucleotide duplex (10 pmol) containing a single dU paired with a deoxyadenine ( Table 1 ) was incubated with a series of EndoVIII and UDG enzyme mixtures for 15 min at 37°C in a 10 μl of T4 DNA ligase reaction buffer (50 mM Tris-HCl pH 7.5, 10 mM MgCl 2 , 10 mM DTT, 1 mM ATP, 20 μg/ml BSA). The reactions were quenched by the addition of 10 μl of 95% formamide, 0.1% xylene cyanol, 0.1% bromophenol blue, 10 mM EDTA, pH 11, and the reaction products were analyzedon a 15% TBE-Urea denaturing gel. S, 34-nt oligonucleotide substrate. P1 and P2, 15 nt and 18 nt cleavage products, respectively. Two product bands of differing size result from the fact that the uracil is not in the centre of the substrate. Lane 1—no enzyme added. Lane 2—reaction contains 0.2 units of UDG. Lane 3—reaction contains 256 ng of EndoVIII. Lanes 4–10, reaction contains 0.2 units of UDG and the amount of EndoVIII shown above the respective lanes.

    Journal: Nucleic Acids Research

    Article Title: USER(TM) friendly DNA engineering and cloning method by uracil excision

    doi: 10.1093/nar/gkm041

    Figure Lengend Snippet: USER enzyme activity assay. A 34-mer oligonucleotide duplex (10 pmol) containing a single dU paired with a deoxyadenine ( Table 1 ) was incubated with a series of EndoVIII and UDG enzyme mixtures for 15 min at 37°C in a 10 μl of T4 DNA ligase reaction buffer (50 mM Tris-HCl pH 7.5, 10 mM MgCl 2 , 10 mM DTT, 1 mM ATP, 20 μg/ml BSA). The reactions were quenched by the addition of 10 μl of 95% formamide, 0.1% xylene cyanol, 0.1% bromophenol blue, 10 mM EDTA, pH 11, and the reaction products were analyzedon a 15% TBE-Urea denaturing gel. S, 34-nt oligonucleotide substrate. P1 and P2, 15 nt and 18 nt cleavage products, respectively. Two product bands of differing size result from the fact that the uracil is not in the centre of the substrate. Lane 1—no enzyme added. Lane 2—reaction contains 0.2 units of UDG. Lane 3—reaction contains 256 ng of EndoVIII. Lanes 4–10, reaction contains 0.2 units of UDG and the amount of EndoVIII shown above the respective lanes.

    Article Snippet: To establish the optimal ratio of the enzymes in the mixture, various amounts (ng) of EndoVIII were pre-mixed with 0.2 units of UDG (New England Biolabs) and the resulting mixtures were assayed for complete nicking of 10 pmol of substrate in 15 min at 37°C in a 10 μl reaction buffer (50 mM Tris-HCl pH 7.5, 10 mM MgCl2 , 10 mM DTT, 1 mM ATP, 20 μg/ml BSA).

    Techniques: Enzyme Activity Assay, Incubation