ntbbvci  (New England Biolabs)


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    Name:
    Nt BbvCI
    Description:
    Nt BbvCI 5 000 units
    Catalog Number:
    R0632L
    Price:
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    Category:
    Restriction Enzymes
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    5 000 units
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    New England Biolabs ntbbvci
    Nt BbvCI
    Nt BbvCI 5 000 units
    https://www.bioz.com/result/ntbbvci/product/New England Biolabs
    Average 98 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    ntbbvci - by Bioz Stars, 2021-05
    98/100 stars

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    Article Title: Identification of hemicatenane-specific binding proteins by fractionation of Hela nuclei extracts
    Article Snippet: T4 polynucleotide kinase, T4 DNA ligase, Nt.BbvcI and Nb.BbvcI nicking enzymes were from New England Biolabs.

    Incubation:

    Article Title: Base-excision repair deficiency alone or combined with increased oxidative stress does not increase mtDNA point mutations in mice
    Article Snippet: .. To visualize different topological isomers of the mtDNA, 400 ng of control total DNA was additionally incubated at 37°C for 30 min with only buffer (no treatment), SacI (linear) (New England Biolabs; 20 U), Nt.BbvCI (nicked circles) (New England Biolabs; 10 U), Topo I (relaxes the closed circles) (New England Biolabs; 5 U), DNA gyrase (compacts the closed circles) (New England Biolabs; 5 U). ..

    Article Title: Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae
    Article Snippet: The blocks were dissolved by 8 U Agarase (Thermo Fisher Scientific) treatment at 42°C overnight. .. In the case of combing of λ phage DNA, site-specific nicks were introduced by Nt.BbvCI nickase cutting 7 times in the phage genome (delimiting 306, 318, 614, 3977, 8013 and 12 451 bp fragments): 1.5 μg λ DNA was incubated with 50 U/ml Nt.BbvCI nickase (New England Biolabs) in 20 μl CutSmart buffer for 30 min at 37°C. ..

    Purification:

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: For the DNA annealing strategy, PCR products obtained with Taq DNA polymerase were treated with T4 DNA polymerase (NEB) for 15 min at 12°C in 1× buffer 2.1 (NEB), to remove 3′-A overhangs. .. Nicking of the DNA and purification of ssDNA Reactions with the nicking endonucleases Nb.BbvCI and Nt.BbvCI were carried out with 2 to 3 μg of DNA in 1× Cutsmart buffer, at 37°C for 2 h. The samples were then purified with the Monarch® PCR & DNA Cleanup Kit (NEB), eluted in 10 μl. ..

    Polymerase Chain Reaction:

    Article Title: High-yield fabrication of DNA and RNA constructs for single molecule force and torque spectroscopy experiments
    Article Snippet: For the DNA annealing strategy, PCR products obtained with Taq DNA polymerase were treated with T4 DNA polymerase (NEB) for 15 min at 12°C in 1× buffer 2.1 (NEB), to remove 3′-A overhangs. .. Nicking of the DNA and purification of ssDNA Reactions with the nicking endonucleases Nb.BbvCI and Nt.BbvCI were carried out with 2 to 3 μg of DNA in 1× Cutsmart buffer, at 37°C for 2 h. The samples were then purified with the Monarch® PCR & DNA Cleanup Kit (NEB), eluted in 10 μl. ..

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    New England Biolabs nt bbvci
    Preparation of a long-branched DNA with methylation. The two plasmids were modified in vivo by M.FnuDII to generate 5′-m5 C GCG, a McrBC recognition sequence {(i), (ii)}. Potential unmethylated plasmids were eliminated by cleavage with BstUI (5′-CGCG). pME63 was cleaved with PvuII and then with nicking endonuclease <t>Nb.BbvCI</t> (iii), while <t>pMap63</t> was treated with nicking endonuclease Nt.BbvCI (iv). The resulting short single strands were dissociated by heating and removed by annealing with a complementary single-strand oligo DNA. The 5′-ends of intermediate (iv) were labeled with 32 P (v), followed by BspHI cleavage for removal of one of the radio-labels (vii). The two DNAs with complementary single-strand regions {(vi), (vii)} were annealed to form a branched structure {viii, eM63(++)} as detailed in ‘Materials and Methods’ section. Open circle, 32 P label at 5′-end; filled diamond, DNA methylation.
    Nt Bbvci, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 98/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/nt bbvci/product/New England Biolabs
    Average 98 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
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    Preparation of a long-branched DNA with methylation. The two plasmids were modified in vivo by M.FnuDII to generate 5′-m5 C GCG, a McrBC recognition sequence {(i), (ii)}. Potential unmethylated plasmids were eliminated by cleavage with BstUI (5′-CGCG). pME63 was cleaved with PvuII and then with nicking endonuclease Nb.BbvCI (iii), while pMap63 was treated with nicking endonuclease Nt.BbvCI (iv). The resulting short single strands were dissociated by heating and removed by annealing with a complementary single-strand oligo DNA. The 5′-ends of intermediate (iv) were labeled with 32 P (v), followed by BspHI cleavage for removal of one of the radio-labels (vii). The two DNAs with complementary single-strand regions {(vi), (vii)} were annealed to form a branched structure {viii, eM63(++)} as detailed in ‘Materials and Methods’ section. Open circle, 32 P label at 5′-end; filled diamond, DNA methylation.

    Journal: Nucleic Acids Research

    Article Title: Cleavage of a model DNA replication fork by a methyl-specific endonuclease

    doi: 10.1093/nar/gkr153

    Figure Lengend Snippet: Preparation of a long-branched DNA with methylation. The two plasmids were modified in vivo by M.FnuDII to generate 5′-m5 C GCG, a McrBC recognition sequence {(i), (ii)}. Potential unmethylated plasmids were eliminated by cleavage with BstUI (5′-CGCG). pME63 was cleaved with PvuII and then with nicking endonuclease Nb.BbvCI (iii), while pMap63 was treated with nicking endonuclease Nt.BbvCI (iv). The resulting short single strands were dissociated by heating and removed by annealing with a complementary single-strand oligo DNA. The 5′-ends of intermediate (iv) were labeled with 32 P (v), followed by BspHI cleavage for removal of one of the radio-labels (vii). The two DNAs with complementary single-strand regions {(vi), (vii)} were annealed to form a branched structure {viii, eM63(++)} as detailed in ‘Materials and Methods’ section. Open circle, 32 P label at 5′-end; filled diamond, DNA methylation.

    Article Snippet: Then it was treated with a nicking enzyme, Nb.BbvCI (New England Biolabs), while pMap63 was nicked with Nt.BbvCI (New England Biolabs).

    Techniques: DNA Methylation Assay, Modification, In Vivo, Sequencing, Labeling

    Interaction between purified SND1 proteins and various DNA constructs. A The organization of SND1 in domains is shown. The double arrow underneath the schematic representation corresponds to the proteins that were expressed in E. coli and purified. The name of the purified protein is indicated on the left side of the double arrow. B Interactions were performed in a final volume of 7.5 μL with 0.1 femtomole of radiolabeled DNA and the indicated amount of purified protein. Species were resolved by electrophoresis under native conditions. Three DNAs were tested for their binding to SND1-64: dsMC09 (lanes 1-5); dsMC10 (lane 6-10); HC (lanes 11-15). Concentrations of protein were as indicated (lanes 1, 6, 11: 0; lanes 2, 7, 12: 0.1 μM; lanes 3, 8, 13: 0.3 μM; lanes 4, 9, 14: 0.9 μM; lanes 5, 10, 15: 2.7 μM). Free DNAs and bound DNAs are indicated. C Interactions were performed in a final volume of 13.25 μL with 0.1 femtomole of radiolabeled DNA and the SDN1-110 at 70 nM. Species were resolved by electrophoresis under native conditions. Three DNAs were tested for their binding to SND1-110: dsMC09 (lanes 1 and 2); dsMC10 (lanes 3 and 4); HC (lanes 5 and 6). Free DNAs and bound DNAs are indicated. D Interactions were as described in (A). The DNA was C10ss, the single stranded circle obtained after nicking of the dsMC10 with Nt.BbvcI. 0.1 femtomole of C10ss was included in the reaction mixture and the concentrations of protein were as indicated (lane 1: 0; lane 2: 0.1 μM; lane 3: 0.3 μM; lane 4: 0.9 μM; lane 5: 2.7 μM). Free DNAs and bound DNAs are indicated. E The two curves (one for HC and one for C10ss) show the percentage of (SDN1-64)-DNA complexes as a function of protein concentration. Error bars correspond to the standard deviation. Percentages are the mean of three independent experiments. F Interactions were as described in (C). C10ss is the single stranded circle obtained after nicking of the dsMC10 with Nt.BbvcI. 0.1 femtomole of C10ss or HC was included in the reaction mixture and the concentration of protein was 70 nM. Free DNAs and bound DNAs are indicated. G The plot shows the percentage of (SDN1-110)-DNA complexes assembled at 70 nM SND1-110. Error bars correspond to the standard deviation. Percentages are the mean of three independent experiments. H The interaction between radiolabeled HC and SND1-64 was tested in the presence of OL21, an oligonucleotide long of 21 nucleotides. SDN1-64 was at 2.7 μM and HC at 14 pM. HC was premixed with increasing amount of OL21 (lane 1: no OL21, no SND1-64; lane 2: no OL21; lane 3: 0.2 nM OL21; lane 4: 0.7 nM OL21; lane 5: 2 nM OL21; lane 6: 7 nM OL21) before adding SND1-64. Free DNAs and bound DNAs are indicated. I The interaction between radiolabeled HC and SND1-110 was tested in the presence of OL21, an oligonucleotide long of 21 nucleotides. SDN1-110 was at 70 nM and HC at 7.5 pM. HC was premixed with increasing amount of OL21 (lane 1: no OL21, no SND1-110; lane 2: no OL21; lane 3: 0.2 nM OL21; lane 4: 0.7 nM OL21; lane 5: 2 nM OL21; lane 6: 7 nM OL21) before adding SND1-110. Species are separated by electrophoresis on a polyacrylamide gel. Free DNAs and bound DNAs are indicated. The plot shows the percentage of (SND1-110)-HC complexes as function of concentration of OL21. The standard deviation is calculated from two independent experiments.

    Journal: bioRxiv

    Article Title: Identification of hemicatenane-specific binding proteins by fractionation of Hela nuclei extracts

    doi: 10.1101/844126

    Figure Lengend Snippet: Interaction between purified SND1 proteins and various DNA constructs. A The organization of SND1 in domains is shown. The double arrow underneath the schematic representation corresponds to the proteins that were expressed in E. coli and purified. The name of the purified protein is indicated on the left side of the double arrow. B Interactions were performed in a final volume of 7.5 μL with 0.1 femtomole of radiolabeled DNA and the indicated amount of purified protein. Species were resolved by electrophoresis under native conditions. Three DNAs were tested for their binding to SND1-64: dsMC09 (lanes 1-5); dsMC10 (lane 6-10); HC (lanes 11-15). Concentrations of protein were as indicated (lanes 1, 6, 11: 0; lanes 2, 7, 12: 0.1 μM; lanes 3, 8, 13: 0.3 μM; lanes 4, 9, 14: 0.9 μM; lanes 5, 10, 15: 2.7 μM). Free DNAs and bound DNAs are indicated. C Interactions were performed in a final volume of 13.25 μL with 0.1 femtomole of radiolabeled DNA and the SDN1-110 at 70 nM. Species were resolved by electrophoresis under native conditions. Three DNAs were tested for their binding to SND1-110: dsMC09 (lanes 1 and 2); dsMC10 (lanes 3 and 4); HC (lanes 5 and 6). Free DNAs and bound DNAs are indicated. D Interactions were as described in (A). The DNA was C10ss, the single stranded circle obtained after nicking of the dsMC10 with Nt.BbvcI. 0.1 femtomole of C10ss was included in the reaction mixture and the concentrations of protein were as indicated (lane 1: 0; lane 2: 0.1 μM; lane 3: 0.3 μM; lane 4: 0.9 μM; lane 5: 2.7 μM). Free DNAs and bound DNAs are indicated. E The two curves (one for HC and one for C10ss) show the percentage of (SDN1-64)-DNA complexes as a function of protein concentration. Error bars correspond to the standard deviation. Percentages are the mean of three independent experiments. F Interactions were as described in (C). C10ss is the single stranded circle obtained after nicking of the dsMC10 with Nt.BbvcI. 0.1 femtomole of C10ss or HC was included in the reaction mixture and the concentration of protein was 70 nM. Free DNAs and bound DNAs are indicated. G The plot shows the percentage of (SDN1-110)-DNA complexes assembled at 70 nM SND1-110. Error bars correspond to the standard deviation. Percentages are the mean of three independent experiments. H The interaction between radiolabeled HC and SND1-64 was tested in the presence of OL21, an oligonucleotide long of 21 nucleotides. SDN1-64 was at 2.7 μM and HC at 14 pM. HC was premixed with increasing amount of OL21 (lane 1: no OL21, no SND1-64; lane 2: no OL21; lane 3: 0.2 nM OL21; lane 4: 0.7 nM OL21; lane 5: 2 nM OL21; lane 6: 7 nM OL21) before adding SND1-64. Free DNAs and bound DNAs are indicated. I The interaction between radiolabeled HC and SND1-110 was tested in the presence of OL21, an oligonucleotide long of 21 nucleotides. SDN1-110 was at 70 nM and HC at 7.5 pM. HC was premixed with increasing amount of OL21 (lane 1: no OL21, no SND1-110; lane 2: no OL21; lane 3: 0.2 nM OL21; lane 4: 0.7 nM OL21; lane 5: 2 nM OL21; lane 6: 7 nM OL21) before adding SND1-110. Species are separated by electrophoresis on a polyacrylamide gel. Free DNAs and bound DNAs are indicated. The plot shows the percentage of (SND1-110)-HC complexes as function of concentration of OL21. The standard deviation is calculated from two independent experiments.

    Article Snippet: T4 polynucleotide kinase, T4 DNA ligase, Nt.BbvcI and Nb.BbvcI nicking enzymes were from New England Biolabs.

    Techniques: Purification, Construct, Electrophoresis, Binding Assay, Protein Concentration, Standard Deviation, Concentration Assay

    Breakage of S. cerevisiae gDNA and λ DNA at preformed ss nicks upon molecular combing. ( A-C ) Molecular combing of nick-translated gDNA from S. cerevisiae . Biotinylated nucleotides were incorporated by nick-translation conducted either in limiting (L), or non-limiting/standard conditions (N), into agarose-embedded gDNA of unperturbed, non-synchronized (A and C), or G1-synchronized (B) BY4741 cells. Biotin was detected by AlexaFluor 647-conjugated anti-biotin antibody (red) and DNA molecules were stained with YOYO-1 (green). Panel D shows examples of co-localization of nicks labeled with TdT (magenta) and R-loops labeled with the RNA:DNA hybrid specific S9.6 antibody (red), when both entities were visualized in the same sample. The percentage of co-labeled spots was estimated ∼10% of all nick-related DNA associated spots. Arrows indicate examples of co-localization. ( E–G ) Molecular combing of λ DNA. Representative images of YOYO-1 stained (green) control (F) and Nt.BbvCI nickase-treated (G) λ DNA. The size distribution histograms of combed DNA molecules before (blue) and after (orange) nickase treatment are shown in panel E. The full length intact ds λ DNA (48.5 kb) corresponds to 16.2 μm (calculated with 3 bp/nm helical repeat length), i.e. the majority of λ DNA molecules were fragmented after combing alone. Images of DNA fibers were assembled from the fields-of-view analyzed, except for panels F and G which show the original fields-of-view. For statistics see Supplementary Tables S1–S5 .

    Journal: Nucleic Acids Research

    Article Title: Endogenous single-strand DNA breaks at RNA polymerase II promoters in Saccharomyces cerevisiae

    doi: 10.1093/nar/gky743

    Figure Lengend Snippet: Breakage of S. cerevisiae gDNA and λ DNA at preformed ss nicks upon molecular combing. ( A-C ) Molecular combing of nick-translated gDNA from S. cerevisiae . Biotinylated nucleotides were incorporated by nick-translation conducted either in limiting (L), or non-limiting/standard conditions (N), into agarose-embedded gDNA of unperturbed, non-synchronized (A and C), or G1-synchronized (B) BY4741 cells. Biotin was detected by AlexaFluor 647-conjugated anti-biotin antibody (red) and DNA molecules were stained with YOYO-1 (green). Panel D shows examples of co-localization of nicks labeled with TdT (magenta) and R-loops labeled with the RNA:DNA hybrid specific S9.6 antibody (red), when both entities were visualized in the same sample. The percentage of co-labeled spots was estimated ∼10% of all nick-related DNA associated spots. Arrows indicate examples of co-localization. ( E–G ) Molecular combing of λ DNA. Representative images of YOYO-1 stained (green) control (F) and Nt.BbvCI nickase-treated (G) λ DNA. The size distribution histograms of combed DNA molecules before (blue) and after (orange) nickase treatment are shown in panel E. The full length intact ds λ DNA (48.5 kb) corresponds to 16.2 μm (calculated with 3 bp/nm helical repeat length), i.e. the majority of λ DNA molecules were fragmented after combing alone. Images of DNA fibers were assembled from the fields-of-view analyzed, except for panels F and G which show the original fields-of-view. For statistics see Supplementary Tables S1–S5 .

    Article Snippet: In the case of combing of λ phage DNA, site-specific nicks were introduced by Nt.BbvCI nickase cutting 7 times in the phage genome (delimiting 306, 318, 614, 3977, 8013 and 12 451 bp fragments): 1.5 μg λ DNA was incubated with 50 U/ml Nt.BbvCI nickase (New England Biolabs) in 20 μl CutSmart buffer for 30 min at 37°C.

    Techniques: Nick Translation, Staining, Labeling

    Heart Sod2 knockout mice show normal mtDNA topology and no decrease in mtDNA copy number. ( A ) Representative phosphorimager exposure of mtDNA topology analysis of total DNA from heart tissue from 10-week old Sod2 loxP x Ckmm cre mice. MtDNA is visualized using radioactive probes towards mtDNA. Control DNA was treated with various enzymes to reveal the different topologies of mtDNA. SacI cuts both strands of mtDNA once (linear), Nt. BbvCI cuts only one strand of mtDNA (nicked), TopoI relaxes the mtDNA (looser coiling), Gyrase creates coiling to mtDNA (compacted supercoiled DNA). Experimental samples are untreated. First gel does not have ethidium bromide (EtBr), second gel has the same samples and EtBr in the gel to compact the closed circle DNA into a quantifiable band. Phosphorimager images are filtered with averaging to reduce noise. Quantifications were made from the original images. ( B ) Quantification of the proportion of closed circle form of mtDNA per total mtDNA. Quantification is done from phosphorimager exposure of the topology gels. White circles indicate samples from controls (pp, n = 11, 9–10 week old) and gray circles indicate samples from Sod2 loxP x Ckmm cre mice (pp,cre, n = 12, 10-week old). ( C ) Relative mtDNA copy number in heart of Sod2 loxP x Ckmm cre mice as assessed with qPCR. MtDNA levels were analyzed with a CytB probe and nuclear DNA with a 18S probe. White circles indicate samples from controls (pp, n = 12, 10–12 week old) and gray circles indicate samples from Sod2 loxP x Ckmm cre mice (pp, cre, n = 11, 10–12 week old). Horizontal lines represent means, error bars represent SD, * P

    Journal: Nucleic Acids Research

    Article Title: Base-excision repair deficiency alone or combined with increased oxidative stress does not increase mtDNA point mutations in mice

    doi: 10.1093/nar/gky456

    Figure Lengend Snippet: Heart Sod2 knockout mice show normal mtDNA topology and no decrease in mtDNA copy number. ( A ) Representative phosphorimager exposure of mtDNA topology analysis of total DNA from heart tissue from 10-week old Sod2 loxP x Ckmm cre mice. MtDNA is visualized using radioactive probes towards mtDNA. Control DNA was treated with various enzymes to reveal the different topologies of mtDNA. SacI cuts both strands of mtDNA once (linear), Nt. BbvCI cuts only one strand of mtDNA (nicked), TopoI relaxes the mtDNA (looser coiling), Gyrase creates coiling to mtDNA (compacted supercoiled DNA). Experimental samples are untreated. First gel does not have ethidium bromide (EtBr), second gel has the same samples and EtBr in the gel to compact the closed circle DNA into a quantifiable band. Phosphorimager images are filtered with averaging to reduce noise. Quantifications were made from the original images. ( B ) Quantification of the proportion of closed circle form of mtDNA per total mtDNA. Quantification is done from phosphorimager exposure of the topology gels. White circles indicate samples from controls (pp, n = 11, 9–10 week old) and gray circles indicate samples from Sod2 loxP x Ckmm cre mice (pp,cre, n = 12, 10-week old). ( C ) Relative mtDNA copy number in heart of Sod2 loxP x Ckmm cre mice as assessed with qPCR. MtDNA levels were analyzed with a CytB probe and nuclear DNA with a 18S probe. White circles indicate samples from controls (pp, n = 12, 10–12 week old) and gray circles indicate samples from Sod2 loxP x Ckmm cre mice (pp, cre, n = 11, 10–12 week old). Horizontal lines represent means, error bars represent SD, * P

    Article Snippet: To visualize different topological isomers of the mtDNA, 400 ng of control total DNA was additionally incubated at 37°C for 30 min with only buffer (no treatment), SacI (linear) (New England Biolabs; 20 U), Nt.BbvCI (nicked circles) (New England Biolabs; 10 U), Topo I (relaxes the closed circles) (New England Biolabs; 5 U), DNA gyrase (compacts the closed circles) (New England Biolabs; 5 U).

    Techniques: Knock-Out, Mouse Assay, Real-time Polymerase Chain Reaction