m0308s  (New England Biolabs)


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  • 84
    Name:
    T4 PDG T4 Endonuclease V
    Description:
    T4 PDG T4 Endonuclease V 2 000 units
    Catalog Number:
    m0308s
    Price:
    75
    Size:
    2 000 units
    Category:
    DNA Glycosylases
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    Structured Review

    New England Biolabs m0308s
    T4 PDG T4 Endonuclease V
    T4 PDG T4 Endonuclease V 2 000 units
    https://www.bioz.com/result/m0308s/product/New England Biolabs
    Average 84 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    m0308s - by Bioz Stars, 2020-01
    84/100 stars

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    Related Articles

    Irradiation:

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: We confirmed the existence of these adducts by the sensitivity of this damaged template to an enzyme called, T4-PDG (from bacteriophage T4, pyrimidine dimer glycosylase; NEB) (Fig. , third lane). .. We observed the following. (1) Several stalled ECs are formed when the DNA is irradiated (Fig. , lane 8 and 5D lane 6). (2) Rho is capable of releasing RNA from the stalled ECs those are in its termination zone only (compare both the panels of Fig. and also supplementary figure ), whereas Mfd releases RNA from all the stalled ECs (Fig. , lanes 9 and 10). (3) Presence of NusG did not change the RNA release pattern of the Rho protein.

    In Vivo:

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: Rho releases RNA from the stalled ECs at the DNA lesions By the virtue of the EC-dislodging properties of Rho, similar phenotypes of the Rho mutants like the mfd − strains and high mutual dependence of both the rho and mfd during the in vivo DNA repair process, strongly indicate that Rho protein is capable of removing the stalled ECs from the DNA lesions in a similar fashion as the Mfd protein. .. We confirmed the existence of these adducts by the sensitivity of this damaged template to an enzyme called, T4-PDG (from bacteriophage T4, pyrimidine dimer glycosylase; NEB) (Fig. , third lane).

    Amplification:

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: Transcription termination assays (i) RNA release assays : To measure the efficacy of the Rho-dependent and Mfd-dependent RNA release from the ECs stalled at the thymine dimers (T–T) made along the template, a linear T7A1-trpt′ DNA template was synthesized by PCR amplification from the plasmid pRS106 using primers RS83 as the forward and RSRK-1 as the reverse primers . .. Formation of T–T dimer were determined from the sensitivity of the UV-exposed template to the enzyme T4-PDG (NEB, USA).

    Agarose Gel Electrophoresis:

    Article Title: Host cell reactivation of gene expression for an adenovirus-encoded reporter gene reflects the repair of UVC-induced cyclobutane pyrimidine dimers and methylene blue plus visible light-induced 8-oxoguanine
    Article Snippet: Prior to treatment of Ad DNA with either T4 pyrimidine-DNA glycosylase [T4pdg; New England Biolabs (NEB) M0308S] or formamidopyrimidine (Fapy)-DNA glycosylase (Fpg; NEB M02040), all samples were digested overnight by 40 units of EcoRI (NEB R0101) in a total reaction volume of 50 µl in 1× NEB buffer 1. .. Following T4pdg treatment, samples were loaded into a 0.8% alkaline agarose gel and separated by electrophoresis (20–24 h at 10 V).

    In Vitro:

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: Formation of T–T dimer were determined from the sensitivity of the UV-exposed template to the enzyme T4-PDG (NEB, USA). .. The UV exposed templates were immobilized on the streptavidin-coated magnetic beads through the 5′-biotin and then used for the in vitro transcription assays.

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: To directly test this proposition, we designed Mfd-induced and Rho-induced in vitro RNA release (a measure of RNAP recycling) assays from the ECs stalled at the DNA lesions (Fig. ). .. We confirmed the existence of these adducts by the sensitivity of this damaged template to an enzyme called, T4-PDG (from bacteriophage T4, pyrimidine dimer glycosylase; NEB) (Fig. , third lane).

    Magnetic Beads:

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: Formation of T–T dimer were determined from the sensitivity of the UV-exposed template to the enzyme T4-PDG (NEB, USA). .. The UV exposed templates were immobilized on the streptavidin-coated magnetic beads through the 5′-biotin and then used for the in vitro transcription assays.

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: On this template, transcription initiates from this promoter and elongates through a Rho-dependent terminator region, trpt’ , and the template is immobilized on the streptavidin-coated magnetic beads via a biotin linkage. .. We confirmed the existence of these adducts by the sensitivity of this damaged template to an enzyme called, T4-PDG (from bacteriophage T4, pyrimidine dimer glycosylase; NEB) (Fig. , third lane).

    Synthesized:

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: Transcription termination assays (i) RNA release assays : To measure the efficacy of the Rho-dependent and Mfd-dependent RNA release from the ECs stalled at the thymine dimers (T–T) made along the template, a linear T7A1-trpt′ DNA template was synthesized by PCR amplification from the plasmid pRS106 using primers RS83 as the forward and RSRK-1 as the reverse primers . .. Formation of T–T dimer were determined from the sensitivity of the UV-exposed template to the enzyme T4-PDG (NEB, USA).

    Sequencing:

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: On this template, the transcription initiates from a strong T7A1 promoter, and contains a T-less sequence in its first 22 bases so that in the absence of UTP in the reaction mixture, a 23-mer stalled elongation complex (EC23 ) could be formed. .. Formation of T–T dimer were determined from the sensitivity of the UV-exposed template to the enzyme T4-PDG (NEB, USA).

    Electrophoresis:

    Article Title: Host cell reactivation of gene expression for an adenovirus-encoded reporter gene reflects the repair of UVC-induced cyclobutane pyrimidine dimers and methylene blue plus visible light-induced 8-oxoguanine
    Article Snippet: Prior to treatment of Ad DNA with either T4 pyrimidine-DNA glycosylase [T4pdg; New England Biolabs (NEB) M0308S] or formamidopyrimidine (Fapy)-DNA glycosylase (Fpg; NEB M02040), all samples were digested overnight by 40 units of EcoRI (NEB R0101) in a total reaction volume of 50 µl in 1× NEB buffer 1. .. Following T4pdg treatment, samples were loaded into a 0.8% alkaline agarose gel and separated by electrophoresis (20–24 h at 10 V).

    Concentration Assay:

    Article Title: Application of the microfluidic-assisted replication track analysis to measure DNA repair in human and mouse cells
    Article Snippet: IdU and CldU were used at a final concentration of 50μM and EdU was used at 10μM. .. T4 PDG endonuclease was purchased from NEB and S1 nuclease from Thermo Scientific.

    Polymerase Chain Reaction:

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: Transcription termination assays (i) RNA release assays : To measure the efficacy of the Rho-dependent and Mfd-dependent RNA release from the ECs stalled at the thymine dimers (T–T) made along the template, a linear T7A1-trpt′ DNA template was synthesized by PCR amplification from the plasmid pRS106 using primers RS83 as the forward and RSRK-1 as the reverse primers . .. Formation of T–T dimer were determined from the sensitivity of the UV-exposed template to the enzyme T4-PDG (NEB, USA).

    Plasmid Preparation:

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions
    Article Snippet: Transcription termination assays (i) RNA release assays : To measure the efficacy of the Rho-dependent and Mfd-dependent RNA release from the ECs stalled at the thymine dimers (T–T) made along the template, a linear T7A1-trpt′ DNA template was synthesized by PCR amplification from the plasmid pRS106 using primers RS83 as the forward and RSRK-1 as the reverse primers . .. Formation of T–T dimer were determined from the sensitivity of the UV-exposed template to the enzyme T4-PDG (NEB, USA).

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    New England Biolabs m0308s
    In vitro transcription assays to measure RNA release. a Cartoon showing the DNA template used for the study. Promoter and the terminator regions are indicated. T–T dimers, generated from the UV-exposure, formed at various sites on the template strands are indicated by (*). ECs with variable RNA chain length are shown to get stalled at the lesions that are located at the proximal most sites from the transcription stat-site. Mfd or Rho dislodges these stalled ECs and release RNA molecules of variable chain length that are analyzed by gel-electrophoresis. Rho loads onto these RNA once the latter reaches the critical lengths of 60–90 nt. Rho and Mfd proteins are indicated. b Autoradiogram showing selective degradation of UV-irradiated DNA by <t>T4-PDG.</t> Radioactive labeled transcription template DNA, with or without UV exposure, was subjected to the cleavage with T4-PDG. c and d Autoradiograms showing in vitro transcription performed on the immobilized DNA templates under different conditions as indicated. S denotes half of the RNA release in the supernatant and P denotes the other half of RNA and the total pellet. Transcripts those reached at the end of the template are denoted as run-off (RO). Zones of RNA release are shown next to the autoradiograms by dashed lines. Fractions of RNA release is calculated as: 2S/([S]+[S+P]). Amounts of RNAP, DNA, Rho, and Mfd were 25, 10, 100, and 100 nM, respectively
    M0308s, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 84/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/m0308s/product/New England Biolabs
    Average 84 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    m0308s - by Bioz Stars, 2020-01
    84/100 stars
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    In vitro transcription assays to measure RNA release. a Cartoon showing the DNA template used for the study. Promoter and the terminator regions are indicated. T–T dimers, generated from the UV-exposure, formed at various sites on the template strands are indicated by (*). ECs with variable RNA chain length are shown to get stalled at the lesions that are located at the proximal most sites from the transcription stat-site. Mfd or Rho dislodges these stalled ECs and release RNA molecules of variable chain length that are analyzed by gel-electrophoresis. Rho loads onto these RNA once the latter reaches the critical lengths of 60–90 nt. Rho and Mfd proteins are indicated. b Autoradiogram showing selective degradation of UV-irradiated DNA by T4-PDG. Radioactive labeled transcription template DNA, with or without UV exposure, was subjected to the cleavage with T4-PDG. c and d Autoradiograms showing in vitro transcription performed on the immobilized DNA templates under different conditions as indicated. S denotes half of the RNA release in the supernatant and P denotes the other half of RNA and the total pellet. Transcripts those reached at the end of the template are denoted as run-off (RO). Zones of RNA release are shown next to the autoradiograms by dashed lines. Fractions of RNA release is calculated as: 2S/([S]+[S+P]). Amounts of RNAP, DNA, Rho, and Mfd were 25, 10, 100, and 100 nM, respectively

    Journal: Nature Communications

    Article Title: Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions

    doi: 10.1038/s41467-019-09146-5

    Figure Lengend Snippet: In vitro transcription assays to measure RNA release. a Cartoon showing the DNA template used for the study. Promoter and the terminator regions are indicated. T–T dimers, generated from the UV-exposure, formed at various sites on the template strands are indicated by (*). ECs with variable RNA chain length are shown to get stalled at the lesions that are located at the proximal most sites from the transcription stat-site. Mfd or Rho dislodges these stalled ECs and release RNA molecules of variable chain length that are analyzed by gel-electrophoresis. Rho loads onto these RNA once the latter reaches the critical lengths of 60–90 nt. Rho and Mfd proteins are indicated. b Autoradiogram showing selective degradation of UV-irradiated DNA by T4-PDG. Radioactive labeled transcription template DNA, with or without UV exposure, was subjected to the cleavage with T4-PDG. c and d Autoradiograms showing in vitro transcription performed on the immobilized DNA templates under different conditions as indicated. S denotes half of the RNA release in the supernatant and P denotes the other half of RNA and the total pellet. Transcripts those reached at the end of the template are denoted as run-off (RO). Zones of RNA release are shown next to the autoradiograms by dashed lines. Fractions of RNA release is calculated as: 2S/([S]+[S+P]). Amounts of RNAP, DNA, Rho, and Mfd were 25, 10, 100, and 100 nM, respectively

    Article Snippet: We confirmed the existence of these adducts by the sensitivity of this damaged template to an enzyme called, T4-PDG (from bacteriophage T4, pyrimidine dimer glycosylase; NEB) (Fig. , third lane).

    Techniques: In Vitro, Generated, Nucleic Acid Electrophoresis, Irradiation, Labeling