bbvci  (New England Biolabs)


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    Structured Review

    New England Biolabs bbvci
    Preparation of a long branched DNA (eF1). ( A ) pES1 was treated with <t>SphI,</t> PvuII and nicking endonuclease <t>Nb.BbvCI.</t> A partial fragment from pGap1 was prepared by PCR with indicated primers, followed by nicking with Nt.BbvCI. ( B ) Single strands between the nicks introduced in the previous step were dissociated by heating with removal by complementary oligo DNA from the fragment containing a gap structure. ( C ) Resulting DNAs with the gap were annealed to form a branched structure (Materials and methods section). A leftward triangle indicates an EcoR124I site, 5′ CGA TGCTGTA TTC . An open circle indicates 32 P for 5′-end labeling.
    Bbvci, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 91/100, based on 27 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bbvci/product/New England Biolabs
    Average 91 stars, based on 27 article reviews
    Price from $9.99 to $1999.99
    bbvci - by Bioz Stars, 2022-09
    91/100 stars

    Images

    1) Product Images from "Cleavage of a model DNA replication fork by a Type I restriction endonuclease"

    Article Title: Cleavage of a model DNA replication fork by a Type I restriction endonuclease

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp214

    Preparation of a long branched DNA (eF1). ( A ) pES1 was treated with SphI, PvuII and nicking endonuclease Nb.BbvCI. A partial fragment from pGap1 was prepared by PCR with indicated primers, followed by nicking with Nt.BbvCI. ( B ) Single strands between the nicks introduced in the previous step were dissociated by heating with removal by complementary oligo DNA from the fragment containing a gap structure. ( C ) Resulting DNAs with the gap were annealed to form a branched structure (Materials and methods section). A leftward triangle indicates an EcoR124I site, 5′ CGA TGCTGTA TTC . An open circle indicates 32 P for 5′-end labeling.
    Figure Legend Snippet: Preparation of a long branched DNA (eF1). ( A ) pES1 was treated with SphI, PvuII and nicking endonuclease Nb.BbvCI. A partial fragment from pGap1 was prepared by PCR with indicated primers, followed by nicking with Nt.BbvCI. ( B ) Single strands between the nicks introduced in the previous step were dissociated by heating with removal by complementary oligo DNA from the fragment containing a gap structure. ( C ) Resulting DNAs with the gap were annealed to form a branched structure (Materials and methods section). A leftward triangle indicates an EcoR124I site, 5′ CGA TGCTGTA TTC . An open circle indicates 32 P for 5′-end labeling.

    Techniques Used: Polymerase Chain Reaction, End Labeling

    2) Product Images from "Biological and molecular characterization of fEg-Eco19, a lytic bacteriophage active against an antibiotic-resistant clinical Escherichia coli isolate"

    Article Title: Biological and molecular characterization of fEg-Eco19, a lytic bacteriophage active against an antibiotic-resistant clinical Escherichia coli isolate

    Journal: Archives of Virology

    doi: 10.1007/s00705-022-05426-6

    Agarose gel electrophoresis analysis of restriction-enzyme-digested fEg-Eco1 9 DNA. Phage genomic DNA was digested with EcoRI (lane 2), Nsil (lane 3), SmaI (lane 4), SalI (lane 5), NruI (lane 6), ClaI (lane 7), AflII (lane 8), and BbvCI (lane 9). Lane 1, undigested DNA. Lane M, 1-kb DNA ladder
    Figure Legend Snippet: Agarose gel electrophoresis analysis of restriction-enzyme-digested fEg-Eco1 9 DNA. Phage genomic DNA was digested with EcoRI (lane 2), Nsil (lane 3), SmaI (lane 4), SalI (lane 5), NruI (lane 6), ClaI (lane 7), AflII (lane 8), and BbvCI (lane 9). Lane 1, undigested DNA. Lane M, 1-kb DNA ladder

    Techniques Used: Agarose Gel Electrophoresis

    3) Product Images from "Determining DNA Supercoiling Enthalpy by Isothermal Titration Calorimetry"

    Article Title: Determining DNA Supercoiling Enthalpy by Isothermal Titration Calorimetry

    Journal: Biochimie

    doi: 10.1016/j.biochi.2012.08.002

    (A) The plasmid map of pXXZ6. Restriction enzyme recognition sites of BamHI, HindIII, and Nt.BbvCI are shown. For supercoiled pXXZ6 used in this study, the supercoiling density was determined to be −0.061. (B) DNA intercalator ethidium bromide
    Figure Legend Snippet: (A) The plasmid map of pXXZ6. Restriction enzyme recognition sites of BamHI, HindIII, and Nt.BbvCI are shown. For supercoiled pXXZ6 used in this study, the supercoiling density was determined to be −0.061. (B) DNA intercalator ethidium bromide

    Techniques Used: Plasmid Preparation

    4) Product Images from "Supercoiling and looping promote DNA base accessibility and coordination among distant sites"

    Article Title: Supercoiling and looping promote DNA base accessibility and coordination among distant sites

    Journal: Nature Communications

    doi: 10.1038/s41467-021-25936-2

    Bal-31 and S1 nuclease cleave at specific DNA sites containing exposed bases. a Map of the 336 bp minicircle sequence showing the positions of the restriction enzymes used, the location of the three major Bal-31/S1 nuclease cleavage sites, and the att R integrase site. The numbers on the inside of the circle indicate the designated start/end of the minicircle sequence (see “Methods”) and also the positions of each restriction site along the listed sequence. Dashed lines indicate the distances between each restriction cleavage site. Intrinsic curvature in att R is centered around the MseI site (Supplementary Fig. 1 ). b Minicircle DNA was cleaved with Bal-31, deproteinized, then subsequently cleaved with each of the restriction enzymes, and the products were separated by agarose gel electrophoresis. The 336 bp Lk = 29; Δ Lk = −3; σ = −0.095 topoisomer is shown. Mr 1 : 100 bp DNA ladder; Mr 2 : low molecular weight DNA ladder; S: supercoiled (336 bp Lk = 29; Δ Lk = −3), N: nicked 336 bp minicircle; L: 336 bp minicircle linearized by EcoRV; -, B, N, M, E, X: minicircle incubated with Bal-31 for 1 min followed by incubation with a second restriction enzyme as indicated (-: no second enzyme; B: BbvCI; N: NdeI; M: MseI; E: EcoRV; X: XmnI). This assay was performed at least two times for each topoisomer with very similar results. c Mapping of S1 nuclease cleavage sites (336 bp; Lk = 29; Δ Lk = −3 topoisomer is shown). The experiment was performed following the same protocol as for Bal-31. This assay was performed once for each topoisomer. d Relative Bal-31 cleavage at each of the three sites as a function of Lk . e Relative S1 nuclease cleavage at each of the three sites as a function of Lk . N.D. not determined. f Model showing localization of sites 1 and 2 to the superhelical apices.
    Figure Legend Snippet: Bal-31 and S1 nuclease cleave at specific DNA sites containing exposed bases. a Map of the 336 bp minicircle sequence showing the positions of the restriction enzymes used, the location of the three major Bal-31/S1 nuclease cleavage sites, and the att R integrase site. The numbers on the inside of the circle indicate the designated start/end of the minicircle sequence (see “Methods”) and also the positions of each restriction site along the listed sequence. Dashed lines indicate the distances between each restriction cleavage site. Intrinsic curvature in att R is centered around the MseI site (Supplementary Fig. 1 ). b Minicircle DNA was cleaved with Bal-31, deproteinized, then subsequently cleaved with each of the restriction enzymes, and the products were separated by agarose gel electrophoresis. The 336 bp Lk = 29; Δ Lk = −3; σ = −0.095 topoisomer is shown. Mr 1 : 100 bp DNA ladder; Mr 2 : low molecular weight DNA ladder; S: supercoiled (336 bp Lk = 29; Δ Lk = −3), N: nicked 336 bp minicircle; L: 336 bp minicircle linearized by EcoRV; -, B, N, M, E, X: minicircle incubated with Bal-31 for 1 min followed by incubation with a second restriction enzyme as indicated (-: no second enzyme; B: BbvCI; N: NdeI; M: MseI; E: EcoRV; X: XmnI). This assay was performed at least two times for each topoisomer with very similar results. c Mapping of S1 nuclease cleavage sites (336 bp; Lk = 29; Δ Lk = −3 topoisomer is shown). The experiment was performed following the same protocol as for Bal-31. This assay was performed once for each topoisomer. d Relative Bal-31 cleavage at each of the three sites as a function of Lk . e Relative S1 nuclease cleavage at each of the three sites as a function of Lk . N.D. not determined. f Model showing localization of sites 1 and 2 to the superhelical apices.

    Techniques Used: Sequencing, Agarose Gel Electrophoresis, Molecular Weight, Incubation

    5) Product Images from "Structural diversity of supercoiled DNA"

    Article Title: Structural diversity of supercoiled DNA

    Journal: Nature Communications

    doi: 10.1038/ncomms9440

    Effect of supercoiling on the structure of minicircle DNA. ( a ) Individual 336 bp minicircle topoisomers were isolated and analysed by polyacrylamide gel electrophoresis in the presence of 10 mM CaCl 2 . Mr: 100 bp DNA ladder, L: minicircle linearized by EcoRV, N: minicircle nicked by Nb.BbvCI. ( b ) Projections of cryo-ET subtomograms of hydrated 336 bp DNA minicircles of the Lk =34 topoisomer. ( c ) Commonly observed shapes were open circle, open figure-8, figure-8, racquet, handcuffs, needle, and rod, each of which are shown in orthogonal views. ( d ) Other shapes observed, especially in the more highly supercoiled topoisomers. ( e ) Shape frequency distribution plot for each topoisomer population (n=number of minicircles analysed). A weighted average for each topoisomer, approximating the average degree of compactness, is denoted by the black triangle. The weighted average was calculated by assigning each conformation a value that increased in line with compactness. Open circles were given a value of 1, open figure-8 s a value of 2, figure-8 s as a value of 3, and so on. The relative fraction of each was subsequently used to determine the average degree of compactness. Lk , Δ Lk and superhelical density (σ) for each topoisomer are shown (see Supplementary Note 1 ).
    Figure Legend Snippet: Effect of supercoiling on the structure of minicircle DNA. ( a ) Individual 336 bp minicircle topoisomers were isolated and analysed by polyacrylamide gel electrophoresis in the presence of 10 mM CaCl 2 . Mr: 100 bp DNA ladder, L: minicircle linearized by EcoRV, N: minicircle nicked by Nb.BbvCI. ( b ) Projections of cryo-ET subtomograms of hydrated 336 bp DNA minicircles of the Lk =34 topoisomer. ( c ) Commonly observed shapes were open circle, open figure-8, figure-8, racquet, handcuffs, needle, and rod, each of which are shown in orthogonal views. ( d ) Other shapes observed, especially in the more highly supercoiled topoisomers. ( e ) Shape frequency distribution plot for each topoisomer population (n=number of minicircles analysed). A weighted average for each topoisomer, approximating the average degree of compactness, is denoted by the black triangle. The weighted average was calculated by assigning each conformation a value that increased in line with compactness. Open circles were given a value of 1, open figure-8 s a value of 2, figure-8 s as a value of 3, and so on. The relative fraction of each was subsequently used to determine the average degree of compactness. Lk , Δ Lk and superhelical density (σ) for each topoisomer are shown (see Supplementary Note 1 ).

    Techniques Used: Isolation, Polyacrylamide Gel Electrophoresis

    6) Product Images from "Sensitive isothermal detection of nucleic-acid sequence by primer generation-rolling circle amplification"

    Article Title: Sensitive isothermal detection of nucleic-acid sequence by primer generation-rolling circle amplification

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkn1014

    Endpoint product analysis of PG–RCA. ( A ) Endpoint products in the presence or absence of 500 amol sample DNA were analyzed on 1.0% agarose gel electrophoresis. The reaction was conducted at 60°C for 30, 45, 60, 75, 90, 105 and 120 min and each reaction was analyzed separately. Lane M was loaded with a 100 bp DNA marker (100, 200, 300, 400, 500/517, 600, 700, 800, 900, 1000, 1200 and 1517 bp from the bottom). ( B ) Endpoint products of 90-min reactions with all or partial reaction components were analyzed on 1.0% agarose gel electrophoresis. DNA, POL and NICK indicate sample DNA, Vent (exo-) DNA polymerase and Nb.BsmI, respectively. Lane M is a 100 bp DNA marker. ( C ) Endpoint product of a 120-min PG–RCA reaction was digested with either BsmI or BbvCI and analyzed on 1.5% agarose gel electrophoresis. Lane ‘-’ was loaded with the 120 min reaction product before restriction enzyme digestion. Lane M is a 100 bp DNA marker.
    Figure Legend Snippet: Endpoint product analysis of PG–RCA. ( A ) Endpoint products in the presence or absence of 500 amol sample DNA were analyzed on 1.0% agarose gel electrophoresis. The reaction was conducted at 60°C for 30, 45, 60, 75, 90, 105 and 120 min and each reaction was analyzed separately. Lane M was loaded with a 100 bp DNA marker (100, 200, 300, 400, 500/517, 600, 700, 800, 900, 1000, 1200 and 1517 bp from the bottom). ( B ) Endpoint products of 90-min reactions with all or partial reaction components were analyzed on 1.0% agarose gel electrophoresis. DNA, POL and NICK indicate sample DNA, Vent (exo-) DNA polymerase and Nb.BsmI, respectively. Lane M is a 100 bp DNA marker. ( C ) Endpoint product of a 120-min PG–RCA reaction was digested with either BsmI or BbvCI and analyzed on 1.5% agarose gel electrophoresis. Lane ‘-’ was loaded with the 120 min reaction product before restriction enzyme digestion. Lane M is a 100 bp DNA marker.

    Techniques Used: Agarose Gel Electrophoresis, Marker

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    New England Biolabs nb bbvci
    Effect of supercoiling on the structure of minicircle DNA. ( a ) Individual 336 bp minicircle topoisomers were isolated and analysed by polyacrylamide gel electrophoresis in the presence of 10 mM CaCl 2 . Mr: 100 bp DNA ladder, L: minicircle linearized by <t>EcoRV,</t> N: minicircle nicked by <t>Nb.BbvCI.</t> ( b ) Projections of cryo-ET subtomograms of hydrated 336 bp DNA minicircles of the Lk =34 topoisomer. ( c ) Commonly observed shapes were open circle, open figure-8, figure-8, racquet, handcuffs, needle, and rod, each of which are shown in orthogonal views. ( d ) Other shapes observed, especially in the more highly supercoiled topoisomers. ( e ) Shape frequency distribution plot for each topoisomer population (n=number of minicircles analysed). A weighted average for each topoisomer, approximating the average degree of compactness, is denoted by the black triangle. The weighted average was calculated by assigning each conformation a value that increased in line with compactness. Open circles were given a value of 1, open figure-8 s a value of 2, figure-8 s as a value of 3, and so on. The relative fraction of each was subsequently used to determine the average degree of compactness. Lk , Δ Lk and superhelical density (σ) for each topoisomer are shown (see Supplementary Note 1 ).
    Nb Bbvci, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 93/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Effect of supercoiling on the structure of minicircle DNA. ( a ) Individual 336 bp minicircle topoisomers were isolated and analysed by polyacrylamide gel electrophoresis in the presence of 10 mM CaCl 2 . Mr: 100 bp DNA ladder, L: minicircle linearized by EcoRV, N: minicircle nicked by Nb.BbvCI. ( b ) Projections of cryo-ET subtomograms of hydrated 336 bp DNA minicircles of the Lk =34 topoisomer. ( c ) Commonly observed shapes were open circle, open figure-8, figure-8, racquet, handcuffs, needle, and rod, each of which are shown in orthogonal views. ( d ) Other shapes observed, especially in the more highly supercoiled topoisomers. ( e ) Shape frequency distribution plot for each topoisomer population (n=number of minicircles analysed). A weighted average for each topoisomer, approximating the average degree of compactness, is denoted by the black triangle. The weighted average was calculated by assigning each conformation a value that increased in line with compactness. Open circles were given a value of 1, open figure-8 s a value of 2, figure-8 s as a value of 3, and so on. The relative fraction of each was subsequently used to determine the average degree of compactness. Lk , Δ Lk and superhelical density (σ) for each topoisomer are shown (see Supplementary Note 1 ).

    Journal: Nature Communications

    Article Title: Structural diversity of supercoiled DNA

    doi: 10.1038/ncomms9440

    Figure Lengend Snippet: Effect of supercoiling on the structure of minicircle DNA. ( a ) Individual 336 bp minicircle topoisomers were isolated and analysed by polyacrylamide gel electrophoresis in the presence of 10 mM CaCl 2 . Mr: 100 bp DNA ladder, L: minicircle linearized by EcoRV, N: minicircle nicked by Nb.BbvCI. ( b ) Projections of cryo-ET subtomograms of hydrated 336 bp DNA minicircles of the Lk =34 topoisomer. ( c ) Commonly observed shapes were open circle, open figure-8, figure-8, racquet, handcuffs, needle, and rod, each of which are shown in orthogonal views. ( d ) Other shapes observed, especially in the more highly supercoiled topoisomers. ( e ) Shape frequency distribution plot for each topoisomer population (n=number of minicircles analysed). A weighted average for each topoisomer, approximating the average degree of compactness, is denoted by the black triangle. The weighted average was calculated by assigning each conformation a value that increased in line with compactness. Open circles were given a value of 1, open figure-8 s a value of 2, figure-8 s as a value of 3, and so on. The relative fraction of each was subsequently used to determine the average degree of compactness. Lk , Δ Lk and superhelical density (σ) for each topoisomer are shown (see Supplementary Note 1 ).

    Article Snippet: BbvCI, EcoRV, Nb.BbvCI, NdeI, Nuclease Bal-31, T4 DNA Ligase, low molecular weight DNA ladder and 100 bp DNA ladder were purchased from New England Biolabs (Ipswich, MA).

    Techniques: Isolation, Polyacrylamide Gel Electrophoresis

    Preparation of a long branched DNA (eF1). ( A ) pES1 was treated with SphI, PvuII and nicking endonuclease Nb.BbvCI. A partial fragment from pGap1 was prepared by PCR with indicated primers, followed by nicking with Nt.BbvCI. ( B ) Single strands between the nicks introduced in the previous step were dissociated by heating with removal by complementary oligo DNA from the fragment containing a gap structure. ( C ) Resulting DNAs with the gap were annealed to form a branched structure (Materials and methods section). A leftward triangle indicates an EcoR124I site, 5′ CGA TGCTGTA TTC . An open circle indicates 32 P for 5′-end labeling.

    Journal: Nucleic Acids Research

    Article Title: Cleavage of a model DNA replication fork by a Type I restriction endonuclease

    doi: 10.1093/nar/gkp214

    Figure Lengend Snippet: Preparation of a long branched DNA (eF1). ( A ) pES1 was treated with SphI, PvuII and nicking endonuclease Nb.BbvCI. A partial fragment from pGap1 was prepared by PCR with indicated primers, followed by nicking with Nt.BbvCI. ( B ) Single strands between the nicks introduced in the previous step were dissociated by heating with removal by complementary oligo DNA from the fragment containing a gap structure. ( C ) Resulting DNAs with the gap were annealed to form a branched structure (Materials and methods section). A leftward triangle indicates an EcoR124I site, 5′ CGA TGCTGTA TTC . An open circle indicates 32 P for 5′-end labeling.

    Article Snippet: BbvCI, SphI and PvuII (New England Biolabs).

    Techniques: Polymerase Chain Reaction, End Labeling

    Agarose gel electrophoresis analysis of restriction-enzyme-digested fEg-Eco1 9 DNA. Phage genomic DNA was digested with EcoRI (lane 2), Nsil (lane 3), SmaI (lane 4), SalI (lane 5), NruI (lane 6), ClaI (lane 7), AflII (lane 8), and BbvCI (lane 9). Lane 1, undigested DNA. Lane M, 1-kb DNA ladder

    Journal: Archives of Virology

    Article Title: Biological and molecular characterization of fEg-Eco19, a lytic bacteriophage active against an antibiotic-resistant clinical Escherichia coli isolate

    doi: 10.1007/s00705-022-05426-6

    Figure Lengend Snippet: Agarose gel electrophoresis analysis of restriction-enzyme-digested fEg-Eco1 9 DNA. Phage genomic DNA was digested with EcoRI (lane 2), Nsil (lane 3), SmaI (lane 4), SalI (lane 5), NruI (lane 6), ClaI (lane 7), AflII (lane 8), and BbvCI (lane 9). Lane 1, undigested DNA. Lane M, 1-kb DNA ladder

    Article Snippet: The purified phage DNA was digested with the restriction endonucleases EcoRI, NsiI, SmaI, SalI, NruI (Thermo Fischer Scientific), ClaI, AflII, and BbvCI (New England Biolabs), which were predicted to produce the best-resolved restriction fragment patterns.

    Techniques: Agarose Gel Electrophoresis

    (A) The plasmid map of pXXZ6. Restriction enzyme recognition sites of BamHI, HindIII, and Nt.BbvCI are shown. For supercoiled pXXZ6 used in this study, the supercoiling density was determined to be −0.061. (B) DNA intercalator ethidium bromide

    Journal: Biochimie

    Article Title: Determining DNA Supercoiling Enthalpy by Isothermal Titration Calorimetry

    doi: 10.1016/j.biochi.2012.08.002

    Figure Lengend Snippet: (A) The plasmid map of pXXZ6. Restriction enzyme recognition sites of BamHI, HindIII, and Nt.BbvCI are shown. For supercoiled pXXZ6 used in this study, the supercoiling density was determined to be −0.061. (B) DNA intercalator ethidium bromide

    Article Snippet: BbvCI, BamHI, and HindIII were purchased from New England Biolabs, Inc. (Beverly, MA).

    Techniques: Plasmid Preparation