phix174  (New England Biolabs)


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    Name:
    PhiX174 RF I DNA
    Description:
    PhiX174 RF I DNA 150 ug
    Catalog Number:
    N3021L
    Price:
    300
    Category:
    Genomic DNA
    Size:
    150 ug
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    Structured Review

    New England Biolabs phix174
    PhiX174 RF I DNA
    PhiX174 RF I DNA 150 ug
    https://www.bioz.com/result/phix174/product/New England Biolabs
    Average 92 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    phix174 - by Bioz Stars, 2021-04
    92/100 stars

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    Related Articles

    Purification:

    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
    Article Snippet: Endo IV assay Assay of Endo IV activity was performed by incubation of enzyme and substrate for 30 min at 37°C in a reaction mixture (20 μl) containing 10 mM Tris–HCl (pH 8.0), 10 mM MgCl2 , 1 mM DTT and BSA (0.1 mg/ml). .. 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. .. The reaction was stopped by the addition of 20 μl of 25 mM EDTA (pH 8.0), and the reaction products were separated by electrophoresis on a 1.0% agarose gel and stained with SYBR Gold (Invitrogen).

    Concentration Assay:

    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
    Article Snippet: Endo IV assay Assay of Endo IV activity was performed by incubation of enzyme and substrate for 30 min at 37°C in a reaction mixture (20 μl) containing 10 mM Tris–HCl (pH 8.0), 10 mM MgCl2 , 1 mM DTT and BSA (0.1 mg/ml). .. 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. .. The reaction was stopped by the addition of 20 μl of 25 mM EDTA (pH 8.0), and the reaction products were separated by electrophoresis on a 1.0% agarose gel and stained with SYBR Gold (Invitrogen).

    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.

    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.

    Incubation:

    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: Topological DNA-binding of structural maintenance of chromosomes-like RecN promotes DNA double-strand break repair in Escherichia coli
    Article Snippet: .. Briefly, the indicated concentrations of RecA were incubated for 10 min on ice in 10 µL buffer SE in the presence of 10 µM phiX174 circular ssDNA (as a nucleotide), and then the indicated concentrations of RecN were added and samples were incubated at 37 °C for 15 min. SSB (2 µM) was added and samples were further incubated for 10 min. .. Reactions were initiated by adding phiX174 linear dsDNA (10 µM as a nucleotide) and then samples were incubated for 90 min or the indicated durations.

    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.

    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.

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    New England Biolabs phix174 rfi
    Phage <t>phiX174</t> DNA survival after MNNG exposure. PhiX174 <t>RFI</t> DNA was incubated with the indicated concentrations of MNNG as described in Materials and Methods and used to transfect strains MV1161 (wild type) and MV3855 ( alkA tagA ) and survival determined by plaque formation.
    Phix174 Rfi, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/phix174 rfi/product/New England Biolabs
    Average 92 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    phix174 rfi - by Bioz Stars, 2021-04
    92/100 stars
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    Phage phiX174 DNA survival after MNNG exposure. PhiX174 RFI DNA was incubated with the indicated concentrations of MNNG as described in Materials and Methods and used to transfect strains MV1161 (wild type) and MV3855 ( alkA tagA ) and survival determined by plaque formation.

    Journal: Nucleic Acids Research

    Article Title: MutS inhibits RecA-mediated strand transfer with methylated DNA substrates

    doi: 10.1093/nar/gki673

    Figure Lengend Snippet: Phage phiX174 DNA survival after MNNG exposure. PhiX174 RFI DNA was incubated with the indicated concentrations of MNNG as described in Materials and Methods and used to transfect strains MV1161 (wild type) and MV3855 ( alkA tagA ) and survival determined by plaque formation.

    Article Snippet: PhiX174 RFI (covalently closed circular) and virion (single-stranded) forms were purchased from New England Biolabs.

    Techniques: Incubation

    Detection of methylated guanines by HPLC-MS/MS. The top three panels are traces of a mixture of the indicated standard compounds while the bottom three panels are traces from formic acid hydrolyzed MNNG treated (300 μM) phiX174 RFI DNA.

    Journal: Nucleic Acids Research

    Article Title: MutS inhibits RecA-mediated strand transfer with methylated DNA substrates

    doi: 10.1093/nar/gki673

    Figure Lengend Snippet: Detection of methylated guanines by HPLC-MS/MS. The top three panels are traces of a mixture of the indicated standard compounds while the bottom three panels are traces from formic acid hydrolyzed MNNG treated (300 μM) phiX174 RFI DNA.

    Article Snippet: PhiX174 RFI (covalently closed circular) and virion (single-stranded) forms were purchased from New England Biolabs.

    Techniques: Methylation, High Performance Liquid Chromatography, Mass Spectrometry

    Isolation and characterization of a new halovirus HHPV-2. ( A ) HHPV-2 plaques on the H. hispanica lawn. ( B ) A representative transmission electron micrograph of negative-stained HHPV-2 virions. Bar, 50 nm. ( C ) DNase I (left) and Mung Bean Nuclease (right) digestions of the HHPV-2 genome, which proved to be an ssDNA molecule. The ssDNA genome (ФX174ss) and replicative form (ФX174ds) of phiX174 were also subjected to digestions. Lane M, dsDNA size marker. ( D ) A schematic depiction of the HHPV-2 genome. Similarities between HHPV-1 [a closely related dsDNA virus ( 23 )] and HHPV-2 homologous gene products are shown. ( E ) Growth curve of uninfected (solid line) and virus-infected (dotted line) H. hispanica DF60 cultures.

    Journal: Nucleic Acids Research

    Article Title: Adaptation of the Haloarcula hispanica CRISPR-Cas system to a purified virus strictly requires a priming process

    doi: 10.1093/nar/gkt1154

    Figure Lengend Snippet: Isolation and characterization of a new halovirus HHPV-2. ( A ) HHPV-2 plaques on the H. hispanica lawn. ( B ) A representative transmission electron micrograph of negative-stained HHPV-2 virions. Bar, 50 nm. ( C ) DNase I (left) and Mung Bean Nuclease (right) digestions of the HHPV-2 genome, which proved to be an ssDNA molecule. The ssDNA genome (ФX174ss) and replicative form (ФX174ds) of phiX174 were also subjected to digestions. Lane M, dsDNA size marker. ( D ) A schematic depiction of the HHPV-2 genome. Similarities between HHPV-1 [a closely related dsDNA virus ( 23 )] and HHPV-2 homologous gene products are shown. ( E ) Growth curve of uninfected (solid line) and virus-infected (dotted line) H. hispanica DF60 cultures.

    Article Snippet: The single-stranded DNA (ssDNA) (ФX174ss) and double-stranded DNA (dsDNA) (ФX174ds) from phiX174 phage (purchased from New England Biolabs) were used as controls.

    Techniques: Isolation, Transmission Assay, Staining, Marker, Infection

    (a) Size exclusion profiles of HvRPA3 in the presence (dashed line) and absence (solid line) of equimolar (based on monomeric protein concentration) 18mer ssDNA in 0.2, 1, and 3 M KCl. The x axis shows elution volume (mls) and the y axis absorbance at 280 nm. Arrows indicate the elution position of ssDNA. (b) Agarose gel retardation assay of HvRPA3 titrated into reactions containing PhiX174 ssDNA. −ve indicates negative control containing no HvRPA3. Increasing quantities of HvRPA3 were used −11, 22, 33, 55, 75, 98, 120, and 125 μ g. Asterisks indicate the concentration-dependent, differentially migrating forms of complex. (c) Titration of the indicated concentrations of HvRPA3 (calculated for monomer due to the potential independence of binding sites in the dimeric form) plotted against normalised FA of the Cy5-labelled 18mer in 1 M (solid line) and 3 M (dashed line) KCl. Data were fitted to a Hill binding model. Produced using GraphPad Prism.

    Journal: Archaea

    Article Title: DNA Binding in High Salt: Analysing the Salt Dependence of Replication Protein A3 from the Halophile Haloferax volcanii

    doi: 10.1155/2012/719092

    Figure Lengend Snippet: (a) Size exclusion profiles of HvRPA3 in the presence (dashed line) and absence (solid line) of equimolar (based on monomeric protein concentration) 18mer ssDNA in 0.2, 1, and 3 M KCl. The x axis shows elution volume (mls) and the y axis absorbance at 280 nm. Arrows indicate the elution position of ssDNA. (b) Agarose gel retardation assay of HvRPA3 titrated into reactions containing PhiX174 ssDNA. −ve indicates negative control containing no HvRPA3. Increasing quantities of HvRPA3 were used −11, 22, 33, 55, 75, 98, 120, and 125 μ g. Asterisks indicate the concentration-dependent, differentially migrating forms of complex. (c) Titration of the indicated concentrations of HvRPA3 (calculated for monomer due to the potential independence of binding sites in the dimeric form) plotted against normalised FA of the Cy5-labelled 18mer in 1 M (solid line) and 3 M (dashed line) KCl. Data were fitted to a Hill binding model. Produced using GraphPad Prism.

    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.

    Techniques: Protein Concentration, Agarose Gel Electrophoresis, Negative Control, Concentration Assay, Titration, Binding Assay, Produced

    Typical DNA force-extension plots. ( A ) The two-site enzyme BsgI tested on the LBAC-B template, which has four recognition sites. The one detected loop had a measured length of 946 bp, in excellent agreement with the separation between the binding sites at positions 8342 and 9287 bp (a distance of 945 bp). ( B ) Sau3AI on the LBAC-A template, which has 55 recognition sites. ( C ) Control experiments: (i) the two-site enzyme Sau3AI was tested on bacteriophage phiX174 DNA, which contains no copies of its recognition sequence; (ii) the one-site enzyme HaeIII was tested on LBAC-B DNA containing 36 copies of its recognition sequence; (iii) the two-site enzyme SfiI was tested on LBAC-B DNA containing one copy of its recognition sequence and (iv) LBAC-B DNA, containing 26 FokI binding sites, incubated in the FokI reaction buffer, but no FokI added.

    Journal: Nucleic Acids Research

    Article Title: DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force

    doi: 10.1093/nar/gkl382

    Figure Lengend Snippet: Typical DNA force-extension plots. ( A ) The two-site enzyme BsgI tested on the LBAC-B template, which has four recognition sites. The one detected loop had a measured length of 946 bp, in excellent agreement with the separation between the binding sites at positions 8342 and 9287 bp (a distance of 945 bp). ( B ) Sau3AI on the LBAC-A template, which has 55 recognition sites. ( C ) Control experiments: (i) the two-site enzyme Sau3AI was tested on bacteriophage phiX174 DNA, which contains no copies of its recognition sequence; (ii) the one-site enzyme HaeIII was tested on LBAC-B DNA containing 36 copies of its recognition sequence; (iii) the two-site enzyme SfiI was tested on LBAC-B DNA containing one copy of its recognition sequence and (iv) LBAC-B DNA, containing 26 FokI binding sites, incubated in the FokI reaction buffer, but no FokI added.

    Article Snippet: PhiX174 DNA was purchased from NEB and was labeled by digesting with XhoI and end-labeling with dATP-14-biotin (Invitrogen).

    Techniques: Binding Assay, Sequencing, Incubation