i rfi circular dsdna  (New England Biolabs)


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    Name:
    PhiX174 RF I DNA
    Description:
    PhiX174 RF I DNA 150 ug
    Catalog Number:
    n3021l
    Price:
    300
    Size:
    150 ug
    Category:
    Genomic DNA
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    Structured Review

    New England Biolabs i rfi circular dsdna
    PhiX174 RF I DNA
    PhiX174 RF I DNA 150 ug
    https://www.bioz.com/result/i rfi circular dsdna/product/New England Biolabs
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    i rfi circular dsdna - by Bioz Stars, 2020-08
    94/100 stars

    Images

    1) Product Images from "Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis"

    Article Title: Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkl553

    Substrate specificity of Endo IV. The activity of Endo IV (1, 0.5, 0.2, 0.1 or 0.05 μg/ml) was assayed with phiX174 RFI circular dsDNA ( A ), phiX174 RFI linear dsDNA ( B ), phiX174 virion circular ssDNA ( C ), linear ssRNA used for the in vitro synthesis of the GST-Endo IV fusion protein ( D ), heat-denatured T4 genomic dsDNA containing gluc-dHMC ( E ), or heat-denatured dC-substituted T4 (T4dC) genomic dsDNA ( F ) as the substrate (5 μg/ml). The reaction products were separated by electrophoresis on a 1.0% agarose gel and stained with SYBR Gold. Lanes M and (–) contain a 1 kb DNA ladder and a reaction mixture incubated in the absence of the enzyme, respectively.
    Figure Legend Snippet: Substrate specificity of Endo IV. The activity of Endo IV (1, 0.5, 0.2, 0.1 or 0.05 μg/ml) was assayed with phiX174 RFI circular dsDNA ( A ), phiX174 RFI linear dsDNA ( B ), phiX174 virion circular ssDNA ( C ), linear ssRNA used for the in vitro synthesis of the GST-Endo IV fusion protein ( D ), heat-denatured T4 genomic dsDNA containing gluc-dHMC ( E ), or heat-denatured dC-substituted T4 (T4dC) genomic dsDNA ( F ) as the substrate (5 μg/ml). The reaction products were separated by electrophoresis on a 1.0% agarose gel and stained with SYBR Gold. Lanes M and (–) contain a 1 kb DNA ladder and a reaction mixture incubated in the absence of the enzyme, respectively.

    Techniques Used: Activity Assay, In Vitro, Electrophoresis, Agarose Gel Electrophoresis, Staining, Incubation

    Related Articles

    Agarose Gel Electrophoresis:

    Article Title: DNA Binding in High Salt: Analysing the Salt Dependence of Replication Protein A3 from the Halophile Haloferax volcanii
    Article Snippet: .. Agarose Gel Retardation 500 ng of PhiX174 ssDNA (New England Biolabs) was incubated with the indicated amounts of HvRPA3 in 20 mM Tris, 15 mM MgCl2 , 2 mM DTT, 50 μ g/mL BSA, 6% glycerol, and 1 M KCl for 10 minutes at 37°C prior to loading on a 0.6% agarose gel. .. Following electrophoresis in 1x TBE buffer, DNA was visualised via ethidium bromide staining under UV illumination.

    Labeling:

    Article Title: DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force
    Article Snippet: .. PhiX174 DNA was purchased from NEB and was labeled by digesting with XhoI and end-labeling with dATP-14-biotin (Invitrogen). .. The DNA was then digested with StuI, purified using the Promega Wizard DNA clean up kit, and end-labeled with dUTP-11-DIG.

    Purification:

    Article Title: In vitro role of Rad54 in Rad51-ssDNA filament-dependent homology search and synaptic complexes formation
    Article Snippet: .. Rad51 at a final concentration of 12 μM (one protein per 3 nt) was introduced into the reaction and incubated 10 min followed by RPA at a final concentration of 1.44 μM (one protein per 25 nt) also during 10 min. Rad54 (wild-type Rad54 or Rad54K341R as stated in the results) and dsDNA (homologous or heterologous, as stated in the results) were added together in a final concentration of 175 nM and 25 nM in molecules of dsDNA (seven proteins per dsDNA molecule) in a final volume of 14 μL during 20 min. For the homologous donor, pUC19 plasmid was used, while PhiX174 RFI was used as heterologous DNA, both purchased from New England Biolabs and purified on MiniQ ion exchange chromatography column. ..

    Concentration Assay:

    Article Title: In vitro role of Rad54 in Rad51-ssDNA filament-dependent homology search and synaptic complexes formation
    Article Snippet: .. Rad51 at a final concentration of 12 μM (one protein per 3 nt) was introduced into the reaction and incubated 10 min followed by RPA at a final concentration of 1.44 μM (one protein per 25 nt) also during 10 min. Rad54 (wild-type Rad54 or Rad54K341R as stated in the results) and dsDNA (homologous or heterologous, as stated in the results) were added together in a final concentration of 175 nM and 25 nM in molecules of dsDNA (seven proteins per dsDNA molecule) in a final volume of 14 μL during 20 min. For the homologous donor, pUC19 plasmid was used, while PhiX174 RFI was used as heterologous DNA, both purchased from New England Biolabs and purified on MiniQ ion exchange chromatography column. ..

    Incubation:

    Article Title: DNA Binding in High Salt: Analysing the Salt Dependence of Replication Protein A3 from the Halophile Haloferax volcanii
    Article Snippet: .. Agarose Gel Retardation 500 ng of PhiX174 ssDNA (New England Biolabs) was incubated with the indicated amounts of HvRPA3 in 20 mM Tris, 15 mM MgCl2 , 2 mM DTT, 50 μ g/mL BSA, 6% glycerol, and 1 M KCl for 10 minutes at 37°C prior to loading on a 0.6% agarose gel. .. Following electrophoresis in 1x TBE buffer, DNA was visualised via ethidium bromide staining under UV illumination.

    Article Title: DNA Binding in High Salt: Analysing the Salt Dependence of Replication Protein A3 from the Halophile Haloferax volcanii
    Article Snippet: .. However, with optimisation, band shifts were observed with agarose gels run in 1× TBE buffer, following incubation of increasing quantities of HvRPA3 with PhiX174 ssDNA in 1 M KCl ( ). ..

    Article Title: In vitro role of Rad54 in Rad51-ssDNA filament-dependent homology search and synaptic complexes formation
    Article Snippet: .. Rad51 at a final concentration of 12 μM (one protein per 3 nt) was introduced into the reaction and incubated 10 min followed by RPA at a final concentration of 1.44 μM (one protein per 25 nt) also during 10 min. Rad54 (wild-type Rad54 or Rad54K341R as stated in the results) and dsDNA (homologous or heterologous, as stated in the results) were added together in a final concentration of 175 nM and 25 nM in molecules of dsDNA (seven proteins per dsDNA molecule) in a final volume of 14 μL during 20 min. For the homologous donor, pUC19 plasmid was used, while PhiX174 RFI was used as heterologous DNA, both purchased from New England Biolabs and purified on MiniQ ion exchange chromatography column. ..

    other:

    Article Title: Cleavage of Bacteriophage ? cI Repressor Involves the RecA C-terminal Domain
    Article Snippet: PhiX174 ssDNA was from New England Biolabs.

    End Labeling:

    Article Title: DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force
    Article Snippet: .. PhiX174 DNA was purchased from NEB and was labeled by digesting with XhoI and end-labeling with dATP-14-biotin (Invitrogen). .. The DNA was then digested with StuI, purified using the Promega Wizard DNA clean up kit, and end-labeled with dUTP-11-DIG.

    Ion Exchange Chromatography:

    Article Title: In vitro role of Rad54 in Rad51-ssDNA filament-dependent homology search and synaptic complexes formation
    Article Snippet: .. Rad51 at a final concentration of 12 μM (one protein per 3 nt) was introduced into the reaction and incubated 10 min followed by RPA at a final concentration of 1.44 μM (one protein per 25 nt) also during 10 min. Rad54 (wild-type Rad54 or Rad54K341R as stated in the results) and dsDNA (homologous or heterologous, as stated in the results) were added together in a final concentration of 175 nM and 25 nM in molecules of dsDNA (seven proteins per dsDNA molecule) in a final volume of 14 μL during 20 min. For the homologous donor, pUC19 plasmid was used, while PhiX174 RFI was used as heterologous DNA, both purchased from New England Biolabs and purified on MiniQ ion exchange chromatography column. ..

    Recombinase Polymerase Amplification:

    Article Title: In vitro role of Rad54 in Rad51-ssDNA filament-dependent homology search and synaptic complexes formation
    Article Snippet: .. Rad51 at a final concentration of 12 μM (one protein per 3 nt) was introduced into the reaction and incubated 10 min followed by RPA at a final concentration of 1.44 μM (one protein per 25 nt) also during 10 min. Rad54 (wild-type Rad54 or Rad54K341R as stated in the results) and dsDNA (homologous or heterologous, as stated in the results) were added together in a final concentration of 175 nM and 25 nM in molecules of dsDNA (seven proteins per dsDNA molecule) in a final volume of 14 μL during 20 min. For the homologous donor, pUC19 plasmid was used, while PhiX174 RFI was used as heterologous DNA, both purchased from New England Biolabs and purified on MiniQ ion exchange chromatography column. ..

    Plasmid Preparation:

    Article Title: In vitro role of Rad54 in Rad51-ssDNA filament-dependent homology search and synaptic complexes formation
    Article Snippet: .. Rad51 at a final concentration of 12 μM (one protein per 3 nt) was introduced into the reaction and incubated 10 min followed by RPA at a final concentration of 1.44 μM (one protein per 25 nt) also during 10 min. Rad54 (wild-type Rad54 or Rad54K341R as stated in the results) and dsDNA (homologous or heterologous, as stated in the results) were added together in a final concentration of 175 nM and 25 nM in molecules of dsDNA (seven proteins per dsDNA molecule) in a final volume of 14 μL during 20 min. For the homologous donor, pUC19 plasmid was used, while PhiX174 RFI was used as heterologous DNA, both purchased from New England Biolabs and purified on MiniQ ion exchange chromatography column. ..

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  • 94
    New England Biolabs i rfi circular dsdna
    Substrate specificity of Endo IV. The activity of Endo IV (1, 0.5, 0.2, 0.1 or 0.05 μg/ml) was assayed with phiX174 <t>RFI</t> circular <t>dsDNA</t> ( A ), phiX174 RFI linear dsDNA ( B ), phiX174 virion circular ssDNA ( C ), linear ssRNA used for the in vitro synthesis of the GST-Endo IV fusion protein ( D ), heat-denatured T4 genomic dsDNA containing gluc-dHMC ( E ), or heat-denatured dC-substituted T4 (T4dC) genomic dsDNA ( F ) as the substrate (5 μg/ml). The reaction products were separated by electrophoresis on a 1.0% agarose gel and stained with SYBR Gold. Lanes M and (–) contain a 1 kb DNA ladder and a reaction mixture incubated in the absence of the enzyme, respectively.
    I Rfi Circular Dsdna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/i rfi circular dsdna/product/New England Biolabs
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    i rfi circular dsdna - by Bioz Stars, 2020-08
    94/100 stars
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    Substrate specificity of Endo IV. The activity of Endo IV (1, 0.5, 0.2, 0.1 or 0.05 μg/ml) was assayed with phiX174 RFI circular dsDNA ( A ), phiX174 RFI linear dsDNA ( B ), phiX174 virion circular ssDNA ( C ), linear ssRNA used for the in vitro synthesis of the GST-Endo IV fusion protein ( D ), heat-denatured T4 genomic dsDNA containing gluc-dHMC ( E ), or heat-denatured dC-substituted T4 (T4dC) genomic dsDNA ( F ) as the substrate (5 μg/ml). The reaction products were separated by electrophoresis on a 1.0% agarose gel and stained with SYBR Gold. Lanes M and (–) contain a 1 kb DNA ladder and a reaction mixture incubated in the absence of the enzyme, respectively.

    Journal: Nucleic Acids Research

    Article Title: Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis

    doi: 10.1093/nar/gkl553

    Figure Lengend Snippet: Substrate specificity of Endo IV. The activity of Endo IV (1, 0.5, 0.2, 0.1 or 0.05 μg/ml) was assayed with phiX174 RFI circular dsDNA ( A ), phiX174 RFI linear dsDNA ( B ), phiX174 virion circular ssDNA ( C ), linear ssRNA used for the in vitro synthesis of the GST-Endo IV fusion protein ( D ), heat-denatured T4 genomic dsDNA containing gluc-dHMC ( E ), or heat-denatured dC-substituted T4 (T4dC) genomic dsDNA ( F ) as the substrate (5 μg/ml). The reaction products were separated by electrophoresis on a 1.0% agarose gel and stained with SYBR Gold. Lanes M and (–) contain a 1 kb DNA ladder and a reaction mixture incubated in the absence of the enzyme, respectively.

    Article Snippet: Purified Endo IV was diluted in a solution containing 10 mM Tris–HCl (pH 8.0), 1 mM DTT and BSA (0.1 mg/ml) and was included in the reaction mixture in a volume of 1 μl. phiX174 replicative form I (RFI) circular dsDNA (New England BioLabs), phiX174 RFI linear dsDNA prepared by PstI digestion, phiX174 virion circular ssDNA (New England BioLabs), linear ssRNA used for synthesis of the GST-Endo IV fusion protein, and heat-denatured T4 or T4dC genomic dsDNA were used as substrates at a final concentration of 5 μg/ml.

    Techniques: Activity Assay, In Vitro, Electrophoresis, Agarose Gel Electrophoresis, Staining, Incubation