bacteriophage φx174 dna  (New England Biolabs)


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    Structured Review

    New England Biolabs bacteriophage φx174 dna
    <t>DNA</t> strand exchange reaction. A scheme of the reaction (a), the temperature (b) and kinetic (c) characteristics, and control reactions (d) are shown. In panels b and c, the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized M13mp18 dsDNA. The latter was added to initiate the reaction after 5 min of preincubation at the temperature indicated. In panel d (homologous controls, lanes 1 to 5), the reaction mixture (20 μl) was the same as described above, but either without RadA Da (lane 1) or with RadA Da degraded by proteinase K (PrK) (lane 2); a complete mixture (lane 3); the same mixture as in lane 3, but without ATP (lane 4); or the same mixture as in lane 3, but without Mg +2 (lane 5). In panel d (heterologous controls, lanes 6 to 8), the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized <t>φX174</t> dsDNA (lane 6) or 8 μM φX174 ssDNA and 16 μM linearized M13mp18 dsDNA (lane 7), or 8 μM φX174 ssDNA and 16 μM linearized φX174 dsDNA (lane 8, showing the strand exchange reaction with φX174 DNA substrates).
    Bacteriophage φx174 Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Efficient Strand Transfer by the RadA Recombinase from the Hyperthermophilic Archaeon Desulfurococcus amylolyticus"

    Article Title: Efficient Strand Transfer by the RadA Recombinase from the Hyperthermophilic Archaeon Desulfurococcus amylolyticus

    Journal: Journal of Bacteriology

    doi:

    DNA strand exchange reaction. A scheme of the reaction (a), the temperature (b) and kinetic (c) characteristics, and control reactions (d) are shown. In panels b and c, the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized M13mp18 dsDNA. The latter was added to initiate the reaction after 5 min of preincubation at the temperature indicated. In panel d (homologous controls, lanes 1 to 5), the reaction mixture (20 μl) was the same as described above, but either without RadA Da (lane 1) or with RadA Da degraded by proteinase K (PrK) (lane 2); a complete mixture (lane 3); the same mixture as in lane 3, but without ATP (lane 4); or the same mixture as in lane 3, but without Mg +2 (lane 5). In panel d (heterologous controls, lanes 6 to 8), the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized φX174 dsDNA (lane 6) or 8 μM φX174 ssDNA and 16 μM linearized M13mp18 dsDNA (lane 7), or 8 μM φX174 ssDNA and 16 μM linearized φX174 dsDNA (lane 8, showing the strand exchange reaction with φX174 DNA substrates).
    Figure Legend Snippet: DNA strand exchange reaction. A scheme of the reaction (a), the temperature (b) and kinetic (c) characteristics, and control reactions (d) are shown. In panels b and c, the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized M13mp18 dsDNA. The latter was added to initiate the reaction after 5 min of preincubation at the temperature indicated. In panel d (homologous controls, lanes 1 to 5), the reaction mixture (20 μl) was the same as described above, but either without RadA Da (lane 1) or with RadA Da degraded by proteinase K (PrK) (lane 2); a complete mixture (lane 3); the same mixture as in lane 3, but without ATP (lane 4); or the same mixture as in lane 3, but without Mg +2 (lane 5). In panel d (heterologous controls, lanes 6 to 8), the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized φX174 dsDNA (lane 6) or 8 μM φX174 ssDNA and 16 μM linearized M13mp18 dsDNA (lane 7), or 8 μM φX174 ssDNA and 16 μM linearized φX174 dsDNA (lane 8, showing the strand exchange reaction with φX174 DNA substrates).

    Techniques Used:

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    Article Title:
    Article Snippet: Bacteriophage φX174 DNA (RFI and circular ssDNA) was obtained from New England Biolabs.

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    New England Biolabs bacteriophage φx174 virion dna
    Diagrams of FEN substrates. (A) Pseudo-Y structure formed by annealing oligonucleotides FS and FA; (B) structure formed by annealing a primer (P-4, P-6, or P-15) to <t>φX174</t> virion <t>DNA</t> and extending; (C) substitution of oligonucleotide FA-T for FA; (D) annealing of oligonucleotide FA-C to FA; (E) annealing of oligonucleotide FS-C to FS; (F) ligation of oligonucleotide FS-L to FS.
    Bacteriophage φx174 Virion Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bacteriophage φx174 virion dna/product/New England Biolabs
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    80
    New England Biolabs double stranded ds phage φx174 dna
    Glycerol gradient sedimentation analysis of the mthMCM preparation. ( A ) The purified HiTrap-Q column fraction of the mthMCM protein (0.1 ml, 75 μg) was loaded onto a 5-ml 15–35% glycerol gradient and centrifuged for 13 hr at 45,000 rpm in a Beckman SW50.1 rotor at 4°C. Eighteen fractions were collected from the bottom, and aliquots (15 μl) of each fraction were loaded onto an SDS/10% polyacrylamide gel, subjected to electrophoresis, and stained with Coomassie blue. Arrows indicate the positions of marker proteins. ( B ) Distribution of <t>DNA</t> helicase activity in glycerol gradient fractions. The assay for helicase activity was carried out with 2 μl of each fraction in reaction mixtures containing 10 fmol of the HS-M substrate (S). P, product. ( C ) Distribution of DNA-dependent ATPase activity. The ATPase activity was assayed in the presence of <t>φX174</t> ssDNA (30 ng/μl), using 2 μl of each fraction.
    Double Stranded Ds Phage φx174 Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    New England Biolabs dna substrates bacteriophage φx174 circular single stranded dna virion
    Strand exchange activity of RecA Ng and RecA Ec at varying levels of Mg 2+ . Reactions were carried out as described in Materials and Methods using completely homologous <t>ΦX174</t> <t>DNA</t> with the indicated levels of Mg 2+ present in the reactions. A representative gel shows aliquots of the strand exchange reactions that were removed and stopped at the times indicated. Nicked circular product (NC) and linear dsDNA (LDS) are noted.
    Dna Substrates Bacteriophage φx174 Circular Single Stranded Dna Virion, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    80
    New England Biolabs bacteriophage φx174 dna
    <t>DNA</t> strand exchange reaction. A scheme of the reaction (a), the temperature (b) and kinetic (c) characteristics, and control reactions (d) are shown. In panels b and c, the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized M13mp18 dsDNA. The latter was added to initiate the reaction after 5 min of preincubation at the temperature indicated. In panel d (homologous controls, lanes 1 to 5), the reaction mixture (20 μl) was the same as described above, but either without RadA Da (lane 1) or with RadA Da degraded by proteinase K (PrK) (lane 2); a complete mixture (lane 3); the same mixture as in lane 3, but without ATP (lane 4); or the same mixture as in lane 3, but without Mg +2 (lane 5). In panel d (heterologous controls, lanes 6 to 8), the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized <t>φX174</t> dsDNA (lane 6) or 8 μM φX174 ssDNA and 16 μM linearized M13mp18 dsDNA (lane 7), or 8 μM φX174 ssDNA and 16 μM linearized φX174 dsDNA (lane 8, showing the strand exchange reaction with φX174 DNA substrates).
    Bacteriophage φx174 Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 80/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bacteriophage φx174 dna/product/New England Biolabs
    Average 80 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    bacteriophage φx174 dna - by Bioz Stars, 2020-08
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    Image Search Results


    Diagrams of FEN substrates. (A) Pseudo-Y structure formed by annealing oligonucleotides FS and FA; (B) structure formed by annealing a primer (P-4, P-6, or P-15) to φX174 virion DNA and extending; (C) substitution of oligonucleotide FA-T for FA; (D) annealing of oligonucleotide FA-C to FA; (E) annealing of oligonucleotide FS-C to FS; (F) ligation of oligonucleotide FS-L to FS.

    Journal: Journal of Bacteriology

    Article Title: Methanococcus jannaschii Flap Endonuclease: Expression, Purification, and Substrate Requirements

    doi:

    Figure Lengend Snippet: Diagrams of FEN substrates. (A) Pseudo-Y structure formed by annealing oligonucleotides FS and FA; (B) structure formed by annealing a primer (P-4, P-6, or P-15) to φX174 virion DNA and extending; (C) substitution of oligonucleotide FA-T for FA; (D) annealing of oligonucleotide FA-C to FA; (E) annealing of oligonucleotide FS-C to FS; (F) ligation of oligonucleotide FS-L to FS.

    Article Snippet: Bacteriophage φX174 virion DNA was purchased from New England Biolabs, Inc. (NEB).

    Techniques: Ligation

    Glycerol gradient sedimentation analysis of the mthMCM preparation. ( A ) The purified HiTrap-Q column fraction of the mthMCM protein (0.1 ml, 75 μg) was loaded onto a 5-ml 15–35% glycerol gradient and centrifuged for 13 hr at 45,000 rpm in a Beckman SW50.1 rotor at 4°C. Eighteen fractions were collected from the bottom, and aliquots (15 μl) of each fraction were loaded onto an SDS/10% polyacrylamide gel, subjected to electrophoresis, and stained with Coomassie blue. Arrows indicate the positions of marker proteins. ( B ) Distribution of DNA helicase activity in glycerol gradient fractions. The assay for helicase activity was carried out with 2 μl of each fraction in reaction mixtures containing 10 fmol of the HS-M substrate (S). P, product. ( C ) Distribution of DNA-dependent ATPase activity. The ATPase activity was assayed in the presence of φX174 ssDNA (30 ng/μl), using 2 μl of each fraction.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum ?H contains DNA helicase activity

    doi:

    Figure Lengend Snippet: Glycerol gradient sedimentation analysis of the mthMCM preparation. ( A ) The purified HiTrap-Q column fraction of the mthMCM protein (0.1 ml, 75 μg) was loaded onto a 5-ml 15–35% glycerol gradient and centrifuged for 13 hr at 45,000 rpm in a Beckman SW50.1 rotor at 4°C. Eighteen fractions were collected from the bottom, and aliquots (15 μl) of each fraction were loaded onto an SDS/10% polyacrylamide gel, subjected to electrophoresis, and stained with Coomassie blue. Arrows indicate the positions of marker proteins. ( B ) Distribution of DNA helicase activity in glycerol gradient fractions. The assay for helicase activity was carried out with 2 μl of each fraction in reaction mixtures containing 10 fmol of the HS-M substrate (S). P, product. ( C ) Distribution of DNA-dependent ATPase activity. The ATPase activity was assayed in the presence of φX174 ssDNA (30 ng/μl), using 2 μl of each fraction.

    Article Snippet: Single-stranded (ss) and double-stranded (ds) phage φX174 DNA and plasmid pUC19 were from New England Biolabs.

    Techniques: Sedimentation, Purification, Electrophoresis, Staining, Marker, Activity Assay

    The mthMCM protein contains DNA-dependent ATPase activity. ( A ) The influence of various DNA preparations on the ATPase activity of the mthMCM protein. The ATPase activity of the multimeric glycerol gradient peak was determined in the absence or presence of the various indicated DNAs (30 ng/μl). The numbers at the bottom of the autoradiogram indicate the amount of 32 P i released (quantitated by phosphorimager analysis). ( B ) Influence of DNA concentration on ATPase activity. ATPase activity assay was measured in the presence of the indicated amount of φX174 ssDNA (○) or pUC19 dsDNA (●) and the mthMCM multimeric glycerol gradient peak fraction (80 ng). The activity observed with no DNA added (5 pmol) was set at a value of 1; ATP hydrolysis in the presence of DNA at various concentrations was calculated relative to this value.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum ?H contains DNA helicase activity

    doi:

    Figure Lengend Snippet: The mthMCM protein contains DNA-dependent ATPase activity. ( A ) The influence of various DNA preparations on the ATPase activity of the mthMCM protein. The ATPase activity of the multimeric glycerol gradient peak was determined in the absence or presence of the various indicated DNAs (30 ng/μl). The numbers at the bottom of the autoradiogram indicate the amount of 32 P i released (quantitated by phosphorimager analysis). ( B ) Influence of DNA concentration on ATPase activity. ATPase activity assay was measured in the presence of the indicated amount of φX174 ssDNA (○) or pUC19 dsDNA (●) and the mthMCM multimeric glycerol gradient peak fraction (80 ng). The activity observed with no DNA added (5 pmol) was set at a value of 1; ATP hydrolysis in the presence of DNA at various concentrations was calculated relative to this value.

    Article Snippet: Single-stranded (ss) and double-stranded (ds) phage φX174 DNA and plasmid pUC19 were from New England Biolabs.

    Techniques: Activity Assay, Concentration Assay

    Strand exchange activity of RecA Ng and RecA Ec at varying levels of Mg 2+ . Reactions were carried out as described in Materials and Methods using completely homologous ΦX174 DNA with the indicated levels of Mg 2+ present in the reactions. A representative gel shows aliquots of the strand exchange reactions that were removed and stopped at the times indicated. Nicked circular product (NC) and linear dsDNA (LDS) are noted.

    Journal: PLoS ONE

    Article Title: Purification and Characterization of the RecA Protein from Neisseria gonorrhoeae

    doi: 10.1371/journal.pone.0017101

    Figure Lengend Snippet: Strand exchange activity of RecA Ng and RecA Ec at varying levels of Mg 2+ . Reactions were carried out as described in Materials and Methods using completely homologous ΦX174 DNA with the indicated levels of Mg 2+ present in the reactions. A representative gel shows aliquots of the strand exchange reactions that were removed and stopped at the times indicated. Nicked circular product (NC) and linear dsDNA (LDS) are noted.

    Article Snippet: DNA substrates Bacteriophage ΦX174 circular single-stranded DNA (virion) (ssDNA) was purchased from New England Biolabs.

    Techniques: Activity Assay

    DNA strand exchange reaction. A scheme of the reaction (a), the temperature (b) and kinetic (c) characteristics, and control reactions (d) are shown. In panels b and c, the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized M13mp18 dsDNA. The latter was added to initiate the reaction after 5 min of preincubation at the temperature indicated. In panel d (homologous controls, lanes 1 to 5), the reaction mixture (20 μl) was the same as described above, but either without RadA Da (lane 1) or with RadA Da degraded by proteinase K (PrK) (lane 2); a complete mixture (lane 3); the same mixture as in lane 3, but without ATP (lane 4); or the same mixture as in lane 3, but without Mg +2 (lane 5). In panel d (heterologous controls, lanes 6 to 8), the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized φX174 dsDNA (lane 6) or 8 μM φX174 ssDNA and 16 μM linearized M13mp18 dsDNA (lane 7), or 8 μM φX174 ssDNA and 16 μM linearized φX174 dsDNA (lane 8, showing the strand exchange reaction with φX174 DNA substrates).

    Journal: Journal of Bacteriology

    Article Title: Efficient Strand Transfer by the RadA Recombinase from the Hyperthermophilic Archaeon Desulfurococcus amylolyticus

    doi:

    Figure Lengend Snippet: DNA strand exchange reaction. A scheme of the reaction (a), the temperature (b) and kinetic (c) characteristics, and control reactions (d) are shown. In panels b and c, the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized M13mp18 dsDNA. The latter was added to initiate the reaction after 5 min of preincubation at the temperature indicated. In panel d (homologous controls, lanes 1 to 5), the reaction mixture (20 μl) was the same as described above, but either without RadA Da (lane 1) or with RadA Da degraded by proteinase K (PrK) (lane 2); a complete mixture (lane 3); the same mixture as in lane 3, but without ATP (lane 4); or the same mixture as in lane 3, but without Mg +2 (lane 5). In panel d (heterologous controls, lanes 6 to 8), the reaction mixture (20 μl) contained TAcMD buffer (pH 7.9), 2.5 mM ATP, 8 μM RadA Da , 8 μM M13mp18 ssDNA, and 16 μM linearized φX174 dsDNA (lane 6) or 8 μM φX174 ssDNA and 16 μM linearized M13mp18 dsDNA (lane 7), or 8 μM φX174 ssDNA and 16 μM linearized φX174 dsDNA (lane 8, showing the strand exchange reaction with φX174 DNA substrates).

    Article Snippet: Bacteriophage φX174 DNA (RFI and circular ssDNA) was obtained from New England Biolabs.

    Techniques: