endonuclease viii  (New England Biolabs)


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    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 endonuclease viii
    Endonuclease VIII
    Endonuclease VIII 5 000 units
    https://www.bioz.com/result/endonuclease viii/product/New England Biolabs
    Average 94 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    endonuclease viii - by Bioz Stars, 2020-07
    94/100 stars

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    Related Articles

    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.

    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 .

    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 [ ].

    Labeling:

    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°C for 1 h. Damage sites are labeled 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°C for 1 h. The Dig-dUTP is covalently incorporated into the DNA for detection of damage sites. .. Cells were then washed in PBS, blocked using 2% BSA in PBS and Dig was then detected using an anti-Dig antibody (abcam #ab420 clone 21H8) at a dilution of 1:250 in 2% BSA in PBS for 1 h at RT.

    Produced:

    Article Title: Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA
    Article Snippet: .. USER enzyme is a proprietary-ratio mixture of UDG and endonuclease VIII (endoVIII) produced by New England Biolabs. ..

    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: Selective enrichment of damaged DNA molecules for ancient genome sequencing
    Article Snippet: .. After washing the beads with 200 μL wash buffer A and 200 μL wash buffer B (see for wash buffer recipes), they were resuspended in an excision reaction mix comprised of the following components: 34.25 μL water, 5 μL 10× GeneAmp PCR buffer II (Life Technologies), 4 μL 25 mM MgCl2 , 1.25 μL 1% Tween-20, 0.5 μL 25 mM dNTP, 0.75 μL 10 U/μL endonuclease VIII, and 0.25 μL 1 U/μL E. coli UDG (both New England Biolabs). ..

    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°C for 1 h. Damage sites are labeled 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°C for 1 h. The Dig-dUTP is covalently incorporated into the DNA for detection of damage sites. .. Cells were then washed in PBS, blocked using 2% BSA in PBS and Dig was then detected using an anti-Dig antibody (abcam #ab420 clone 21H8) at a dilution of 1:250 in 2% BSA in PBS for 1 h at RT.

    Activity Assay:

    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°C for 1 h. Damage sites are labeled 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°C for 1 h. The Dig-dUTP is covalently incorporated into the DNA for detection of damage sites. .. Cells were then washed in PBS, blocked using 2% BSA in PBS and Dig was then detected using an anti-Dig antibody (abcam #ab420 clone 21H8) at a dilution of 1:250 in 2% BSA in PBS for 1 h at RT.

    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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  • 99
    New England Biolabs restriction endonuclease bstz17 i
    A – Non-radioactive PCR-SSCP analysis of VHL exon 3; T – altered mobility observed in a tumor sample, relative to the normal control N. B – Ethidium bromide-stained polyacrylamide gel of <t>BstZ17</t> I restriction digestion. Lane 1 – peripheral venous blood, Lane 2 – renal cell carcinoma, Lane 3 – non tumoral tissue from kidney, Lane 4 – thyroid metastases, M – denotes the lane containing the pUC Mix Marker 8 (Fermentas, Burlingyon, Canada). For the wild allele, restriction digestion produces bands of 212 and 59 bp. The mutation abolishes the restriction site and the mutant allele corresponds to a 271 bp band. C and D – Tumour DNA sequence in the VHL codon 156 region of cloned exon 3 amplicons. As a consequence of the 680 delA, a premature stop codon appears in the mutant allele.
    Restriction Endonuclease Bstz17 I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/restriction endonuclease bstz17 i/product/New England Biolabs
    Average 99 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    restriction endonuclease bstz17 i - by Bioz Stars, 2020-07
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    A – Non-radioactive PCR-SSCP analysis of VHL exon 3; T – altered mobility observed in a tumor sample, relative to the normal control N. B – Ethidium bromide-stained polyacrylamide gel of BstZ17 I restriction digestion. Lane 1 – peripheral venous blood, Lane 2 – renal cell carcinoma, Lane 3 – non tumoral tissue from kidney, Lane 4 – thyroid metastases, M – denotes the lane containing the pUC Mix Marker 8 (Fermentas, Burlingyon, Canada). For the wild allele, restriction digestion produces bands of 212 and 59 bp. The mutation abolishes the restriction site and the mutant allele corresponds to a 271 bp band. C and D – Tumour DNA sequence in the VHL codon 156 region of cloned exon 3 amplicons. As a consequence of the 680 delA, a premature stop codon appears in the mutant allele.

    Journal: BMC Endocrine Disorders

    Article Title: A multinodular goiter as the initial presentation of a renal cell carcinoma harbouring a novel VHL mutation

    doi: 10.1186/1472-6823-6-6

    Figure Lengend Snippet: A – Non-radioactive PCR-SSCP analysis of VHL exon 3; T – altered mobility observed in a tumor sample, relative to the normal control N. B – Ethidium bromide-stained polyacrylamide gel of BstZ17 I restriction digestion. Lane 1 – peripheral venous blood, Lane 2 – renal cell carcinoma, Lane 3 – non tumoral tissue from kidney, Lane 4 – thyroid metastases, M – denotes the lane containing the pUC Mix Marker 8 (Fermentas, Burlingyon, Canada). For the wild allele, restriction digestion produces bands of 212 and 59 bp. The mutation abolishes the restriction site and the mutant allele corresponds to a 271 bp band. C and D – Tumour DNA sequence in the VHL codon 156 region of cloned exon 3 amplicons. As a consequence of the 680 delA, a premature stop codon appears in the mutant allele.

    Article Snippet: Restriction analysis, using the restriction endonuclease BstZ17 I (New England BioLabs® , Inc., Beverly, USA) was also performed.

    Techniques: Polymerase Chain Reaction, Staining, Marker, Mutagenesis, Sequencing, Clone Assay

    PFGE patterns of Xba I-restricted DNA from ESBL-producing K. pneumoniae . Lanes: A, clinical strain L-51 from Laënnec Hospital; B, clinical strain N-69 from Necker Hospital; C to J, clinical strains 93-1, 93-2, 93-3, 93-4, 93-5, 93-6, 93-7, and 93-8, isolated from the outbreak in the Department of Obstetrics and Gynecology; K, strain 93-9, isolated from the ultrasonography coupling gel container; L and M, clinical strains B-93a and B-93b, isolated from other wards of Boucicaut Hospital in July and October 1993.

    Journal: Journal of Clinical Microbiology

    Article Title: Nosocomial Outbreak of Klebsiella pneumoniae Producing SHV-5 Extended-Spectrum ?-Lactamase, Originating from a Contaminated Ultrasonography Coupling Gel

    doi:

    Figure Lengend Snippet: PFGE patterns of Xba I-restricted DNA from ESBL-producing K. pneumoniae . Lanes: A, clinical strain L-51 from Laënnec Hospital; B, clinical strain N-69 from Necker Hospital; C to J, clinical strains 93-1, 93-2, 93-3, 93-4, 93-5, 93-6, 93-7, and 93-8, isolated from the outbreak in the Department of Obstetrics and Gynecology; K, strain 93-9, isolated from the ultrasonography coupling gel container; L and M, clinical strains B-93a and B-93b, isolated from other wards of Boucicaut Hospital in July and October 1993.

    Article Snippet: DNA was cleaved overnight with restriction endonuclease Xba I according to the manufacturer’s recommendations (New England Biolabs).

    Techniques: Isolation

    Effect of plasmid DNA conformation on DNA measurement methods. (A) Comparison of various methods on supercoiled plasmid DNA quantification. (B) Hoechst dye-based DNA quantification method. (C) Quant-iT dsDNA BR quantification assay. (D) OD 260 DNA quantification method. S-LB: supercoiled plasmid treated with SspI reaction buffer. S-NB: supercoiled plasmid treated with Nt.BspQI reaction buffer. S-CB: supercoiled plasmid treated with topoisomerase I reaction buffer. a, b, c, d and e : groups with significant difference to each other (Duncan's multiple range test, P

    Journal: PLoS ONE

    Article Title: Quantification Bias Caused by Plasmid DNA Conformation in Quantitative Real-Time PCR Assay

    doi: 10.1371/journal.pone.0029101

    Figure Lengend Snippet: Effect of plasmid DNA conformation on DNA measurement methods. (A) Comparison of various methods on supercoiled plasmid DNA quantification. (B) Hoechst dye-based DNA quantification method. (C) Quant-iT dsDNA BR quantification assay. (D) OD 260 DNA quantification method. S-LB: supercoiled plasmid treated with SspI reaction buffer. S-NB: supercoiled plasmid treated with Nt.BspQI reaction buffer. S-CB: supercoiled plasmid treated with topoisomerase I reaction buffer. a, b, c, d and e : groups with significant difference to each other (Duncan's multiple range test, P

    Article Snippet: Linear (L), close circular (C) and nicked-circular (N) form plasmids were prepared from supercoiled plasmids using restriction endonuclease SspI (NEW ENGLAND Biolabs, Inc., Ipswich, MA, USA), topoisomerase I (NEW ENGLAND Biolabs) and nicking endonuclease Nt.BspQI (NEW ENGLAND Biolabs), respectively.

    Techniques: Plasmid Preparation

    Preparation of plasmid samples. Lane M: 1 kb ladder DNA marker. Lane 1: S, supercoiled plasmid sample. Lane 2: L, linear plasmid sample (SspI treated). Lane 3: N, nicked-circular plasmid sample (Nt.BspQI treated). Lane 4: C, closed-circular plasmid sample (topoisomerase I treated). Lane 5: S-LB, supercoiled plasmid treated with SspI reaction buffer. Lane 6: S-NB, supercoiled plasmid treated with Nt.BspQI reaction buffer. Lane 7: S-CB, supercoiled plasmid treated with topoisomerase I reaction buffer.

    Journal: PLoS ONE

    Article Title: Quantification Bias Caused by Plasmid DNA Conformation in Quantitative Real-Time PCR Assay

    doi: 10.1371/journal.pone.0029101

    Figure Lengend Snippet: Preparation of plasmid samples. Lane M: 1 kb ladder DNA marker. Lane 1: S, supercoiled plasmid sample. Lane 2: L, linear plasmid sample (SspI treated). Lane 3: N, nicked-circular plasmid sample (Nt.BspQI treated). Lane 4: C, closed-circular plasmid sample (topoisomerase I treated). Lane 5: S-LB, supercoiled plasmid treated with SspI reaction buffer. Lane 6: S-NB, supercoiled plasmid treated with Nt.BspQI reaction buffer. Lane 7: S-CB, supercoiled plasmid treated with topoisomerase I reaction buffer.

    Article Snippet: Linear (L), close circular (C) and nicked-circular (N) form plasmids were prepared from supercoiled plasmids using restriction endonuclease SspI (NEW ENGLAND Biolabs, Inc., Ipswich, MA, USA), topoisomerase I (NEW ENGLAND Biolabs) and nicking endonuclease Nt.BspQI (NEW ENGLAND Biolabs), respectively.

    Techniques: Plasmid Preparation, Marker

    Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved Taq α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .

    Journal: PLoS ONE

    Article Title: Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy

    doi: 10.1371/journal.pone.0087053

    Figure Lengend Snippet: Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved Taq α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .

    Article Snippet: Approximately 5 µg of DNA was digested by 30 units Taq α I restriction endonuclease (New England BioLabs, Inc.) according to the manufacturer’s instructions.

    Techniques: Sequencing

    Manhattan plot of la1-mu1 Taq α I sequencing. ( A ) Manhattan plot showing the distribution of reads from la1-mu1 genomic DNA mapped throughout the B73 genome. Alternating colors represent each of the ten maize chromosomes. Each x-axis pixel represents a bin of 1 Mb and the logarithmic y-axis denotes the number of reads mapping to each bin. The red line represents the known genetic map position for the la1 reference mutation. Each triangle below the plot represents the approximate location of mapped MFS. ( B ) Expanded Manhattan plot of a 1 Mb interval corresponding to the approximate map position of la1 . Same as top with each x-axis pixel representing a bin of 1 kb. Filtered genes in the 1 Mb interval are shown as black rectangles. MFS mapping to this interval are shown as inverted red triangles.

    Journal: PLoS ONE

    Article Title: Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy

    doi: 10.1371/journal.pone.0087053

    Figure Lengend Snippet: Manhattan plot of la1-mu1 Taq α I sequencing. ( A ) Manhattan plot showing the distribution of reads from la1-mu1 genomic DNA mapped throughout the B73 genome. Alternating colors represent each of the ten maize chromosomes. Each x-axis pixel represents a bin of 1 Mb and the logarithmic y-axis denotes the number of reads mapping to each bin. The red line represents the known genetic map position for the la1 reference mutation. Each triangle below the plot represents the approximate location of mapped MFS. ( B ) Expanded Manhattan plot of a 1 Mb interval corresponding to the approximate map position of la1 . Same as top with each x-axis pixel representing a bin of 1 kb. Filtered genes in the 1 Mb interval are shown as black rectangles. MFS mapping to this interval are shown as inverted red triangles.

    Article Snippet: Approximately 5 µg of DNA was digested by 30 units Taq α I restriction endonuclease (New England BioLabs, Inc.) according to the manufacturer’s instructions.

    Techniques: Sequencing, Mutagenesis

    Mu - Taq α I Library Construction. Digesting genomic DNA with Taq α I creates a library of fragments. Fragments containing a Mu -MFS junction will all contain a degenerate 39 nt Mu TIR tag along with 31–35 nt of flanking genomic sequence at one end of the 2×75 nt paired-end read. These fragments are computationally identified and the Mu flanking sequence (MFS) is mapped to the maize reference genome.

    Journal: PLoS ONE

    Article Title: Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy

    doi: 10.1371/journal.pone.0087053

    Figure Lengend Snippet: Mu - Taq α I Library Construction. Digesting genomic DNA with Taq α I creates a library of fragments. Fragments containing a Mu -MFS junction will all contain a degenerate 39 nt Mu TIR tag along with 31–35 nt of flanking genomic sequence at one end of the 2×75 nt paired-end read. These fragments are computationally identified and the Mu flanking sequence (MFS) is mapped to the maize reference genome.

    Article Snippet: Approximately 5 µg of DNA was digested by 30 units Taq α I restriction endonuclease (New England BioLabs, Inc.) according to the manufacturer’s instructions.

    Techniques: Sequencing