t7 exonuclease Search Results


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  • 97
    New England Biolabs t7 exonuclease
    Ku and DNA ligase IV–XRCC4 separately and in combination can protect against <t>T7</t> exonuclease digestion. T7 exonuclease (5 U) in the absence or presence of Ku and/or DNA ligase IV–XRCC4, as indicated, was incubated with an end-labeled substrate having cohesive ends (top) or blunt ends (bottom), and the products were analyzed by electrophoresis and autoradiography. The results shown are representive of three experiments undertaken, and the percentage recovery of the label represents the mean of the three experiments. Lane 1, control substrate; lane 2, substrate + 5 U of T7 exonuclease; lanes 3–8, substrate with T7 exonuclease and Ku and/or DNA ligase IV–XRCC4 as indicated.
    T7 Exonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 97/100, based on 217 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t7 exonuclease/product/New England Biolabs
    Average 97 stars, based on 217 article reviews
    Price from $9.99 to $1999.99
    t7 exonuclease - by Bioz Stars, 2020-08
    97/100 stars
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    92
    Thermo Fisher t7 exonuclease
    Ku and DNA ligase IV–XRCC4 separately and in combination can protect against <t>T7</t> exonuclease digestion. T7 exonuclease (5 U) in the absence or presence of Ku and/or DNA ligase IV–XRCC4, as indicated, was incubated with an end-labeled substrate having cohesive ends (top) or blunt ends (bottom), and the products were analyzed by electrophoresis and autoradiography. The results shown are representive of three experiments undertaken, and the percentage recovery of the label represents the mean of the three experiments. Lane 1, control substrate; lane 2, substrate + 5 U of T7 exonuclease; lanes 3–8, substrate with T7 exonuclease and Ku and/or DNA ligase IV–XRCC4 as indicated.
    T7 Exonuclease, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 38 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t7 exonuclease/product/Thermo Fisher
    Average 92 stars, based on 38 article reviews
    Price from $9.99 to $1999.99
    t7 exonuclease - by Bioz Stars, 2020-08
    92/100 stars
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    88
    GE Healthcare t7 gene 6 exonuclease
    Different RecE/RecT and Redα/Redβ recombination mechanisms revealed by different substrates. ( A ) Relative recombination efficiencies achieved using RecE/RecT (ET) or Redα/Redβ (βα) expression constructs in either JC5547 or JC5519 as indicated, as a function of homology region length, are shown. Linear molecules, which were generated to contain homology regions of variable length at their ends, were allowed to recombine with a prelinearized target generated by restriction digestion. Recombination efficiencies from one experiment are shown relative to the maximum recombination efficiency of  B , which was set to 1. Recombination efficiencies are thus presented as relative and are not directly comparable to those shown in previous figures. The experiment was repeated twice, producing similar results. (█) 5547ET; (○) 5519ET; (●) 5547βα; (□) 5519βα. ( B ) Same as  A , except that the target was left intact. The maximum absolute recombination efficiency found was arbitrarily set to 1, and all other recombination efficiencies were related to this maximum. Recombination efficiencies from one experiment are shown. The experiment was repeated five times, producing similar results. The experiments shown in  A  and  B  were done in parallel with the same batches of competent cells and PCR fragments. Colony numbers observed in these experiments were adjusted to relative recombination efficiencies by relating to the maximums obtained in  B , which were set to 1. (█) 5547ET; (○) 5519ET; (●) 5547βα; (□) 5519βα. ( C ) Recombination efficiencies in the presence of the indicated expression constructs in JC5519 using two linear molecules, both of which were preresected in vitro using T7 gene six exonuclease. Data from one representative experiment is shown, in which pools of preresected molecules (which shared 400 nucleotide homology regions and were generated using six different incubation conditions with T7 gene 6 exonuclease) were recombined. C, no exogenous protein expressed; β, expression of Redβ only; βα, coexpression of Redβ and Redα; T, expression of RecT only; ET, coexpression of RecE and RecT. Recombination efficiencies are shown relative to the maximum of  B .
    T7 Gene 6 Exonuclease, supplied by GE Healthcare, used in various techniques. Bioz Stars score: 88/100, based on 25 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t7 gene 6 exonuclease/product/GE Healthcare
    Average 88 stars, based on 25 article reviews
    Price from $9.99 to $1999.99
    t7 gene 6 exonuclease - by Bioz Stars, 2020-08
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    99
    New England Biolabs t7 exonuclease treatment cutsmart buffer
    Different RecE/RecT and Redα/Redβ recombination mechanisms revealed by different substrates. ( A ) Relative recombination efficiencies achieved using RecE/RecT (ET) or Redα/Redβ (βα) expression constructs in either JC5547 or JC5519 as indicated, as a function of homology region length, are shown. Linear molecules, which were generated to contain homology regions of variable length at their ends, were allowed to recombine with a prelinearized target generated by restriction digestion. Recombination efficiencies from one experiment are shown relative to the maximum recombination efficiency of  B , which was set to 1. Recombination efficiencies are thus presented as relative and are not directly comparable to those shown in previous figures. The experiment was repeated twice, producing similar results. (█) 5547ET; (○) 5519ET; (●) 5547βα; (□) 5519βα. ( B ) Same as  A , except that the target was left intact. The maximum absolute recombination efficiency found was arbitrarily set to 1, and all other recombination efficiencies were related to this maximum. Recombination efficiencies from one experiment are shown. The experiment was repeated five times, producing similar results. The experiments shown in  A  and  B  were done in parallel with the same batches of competent cells and PCR fragments. Colony numbers observed in these experiments were adjusted to relative recombination efficiencies by relating to the maximums obtained in  B , which were set to 1. (█) 5547ET; (○) 5519ET; (●) 5547βα; (□) 5519βα. ( C ) Recombination efficiencies in the presence of the indicated expression constructs in JC5519 using two linear molecules, both of which were preresected in vitro using T7 gene six exonuclease. Data from one representative experiment is shown, in which pools of preresected molecules (which shared 400 nucleotide homology regions and were generated using six different incubation conditions with T7 gene 6 exonuclease) were recombined. C, no exogenous protein expressed; β, expression of Redβ only; βα, coexpression of Redβ and Redα; T, expression of RecT only; ET, coexpression of RecE and RecT. Recombination efficiencies are shown relative to the maximum of  B .
    T7 Exonuclease Treatment Cutsmart Buffer, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/t7 exonuclease treatment cutsmart buffer/product/New England Biolabs
    Average 99 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    t7 exonuclease treatment cutsmart buffer - by Bioz Stars, 2020-08
    99/100 stars
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    99
    New England Biolabs exonuclease t7
    Dual biotin-labeled DNA fragments form a closed substrate on the surface of the BLI probe. (A) A schematic of a double digestion assay using <t>Exonuclease</t> T7 + Exonuclease VII and PCR. PCR was performed using M13F, M13R oligos, and DNA attached to the BLI surface as a template. (B) The BLI probe was severed from the plastic adaptor and immerged into a PCR master mix. (C) Dual biotin-labeled DNA fragments on the BLI surface were resistant to Exo T7 + Exo VII digestion while single biotin-labeled DNA fragments on the BLI surface were not.
    Exonuclease T7, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease t7/product/New England Biolabs
    Average 99 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    exonuclease t7 - by Bioz Stars, 2020-08
    99/100 stars
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    Image Search Results


    Ku and DNA ligase IV–XRCC4 separately and in combination can protect against T7 exonuclease digestion. T7 exonuclease (5 U) in the absence or presence of Ku and/or DNA ligase IV–XRCC4, as indicated, was incubated with an end-labeled substrate having cohesive ends (top) or blunt ends (bottom), and the products were analyzed by electrophoresis and autoradiography. The results shown are representive of three experiments undertaken, and the percentage recovery of the label represents the mean of the three experiments. Lane 1, control substrate; lane 2, substrate + 5 U of T7 exonuclease; lanes 3–8, substrate with T7 exonuclease and Ku and/or DNA ligase IV–XRCC4 as indicated.

    Journal: Nucleic Acids Research

    Article Title: Impact of DNA ligase IV on the fidelity of end joining in human cells

    doi:

    Figure Lengend Snippet: Ku and DNA ligase IV–XRCC4 separately and in combination can protect against T7 exonuclease digestion. T7 exonuclease (5 U) in the absence or presence of Ku and/or DNA ligase IV–XRCC4, as indicated, was incubated with an end-labeled substrate having cohesive ends (top) or blunt ends (bottom), and the products were analyzed by electrophoresis and autoradiography. The results shown are representive of three experiments undertaken, and the percentage recovery of the label represents the mean of the three experiments. Lane 1, control substrate; lane 2, substrate + 5 U of T7 exonuclease; lanes 3–8, substrate with T7 exonuclease and Ku and/or DNA ligase IV–XRCC4 as indicated.

    Article Snippet: We also show that DNA ligase IV–XRCC4 can contribute to the protection of ends from degradation by T7 exonuclease.

    Techniques: Incubation, Labeling, Electrophoresis, Autoradiography

    Elongation Complex Footprint and Mapping of the Transcription Bubble (A) (Upper) Summary of elongation complex preparation, drawn to scale. (Lower) Elongation complexes with 5′ end-labeled, 131-mer transcribed DNA were digested with increasing amounts of DNase I, as indicated. The footprint region where DNase I cleavage is repressed (bold line) and a hypersensitive site (sphere) are indicated on the right. M, thymine-specific cleavage marker. Elongation complex (oval) and RNA (bold line) are indicated on the left. Position of the active site is taken as +1. (B) (Upper) Schematic diagram of the locations of the RNA primer (bold text) and G stop (gray box) in the elongation complex. The 150-mer transcribed strand (TS), the corresponding end-labeled nontranscribed strand (NTS), and the direction of exonuclease digestion are indicated. (Lower) Elongation complexes incubated alone, or with ATP/UTP/GTP and TFIIS, were digested with T7 exonuclease to mark their position(s), modified with increasing amounts of KMnO 4 (2 and 8 mM), and analyzed by denaturing PAGE (lanes 1–4). Bands corresponding to the major elongation complexes (2 mM KMnO 4 experiment shown) were isolated, cleaved at modified thymines with piperidine, and resolved by denaturing PAGE (lanes 5 and 6). DNA sequence is shown on the left. Spheres, modified thymines. Arrowheads, positions of active sites. (C) Crystal structure of the elongation complex with modeled DNA paths (dashed lines). Space-filling model shows the DNA (color) engulfed in protein bulk. (D) Area protected by RNAPII (DNase I footprinting, solid line; crystallography model, dashed line) and their transcription bubbles. Only reconstituted elongation complex was mapped by DNase I footprinting. However, T7 exonuclease digests to the same distance from the edge of the two footprints (±1 base; positions indicated by vertical arrow) before and after transcription, showing that RNAPII moved forward upon NTP addition.

    Journal: Molecular Cell

    Article Title: Stability, Flexibility, and Dynamic Interactions of Colliding RNA Polymerase II Elongation Complexes

    doi: 10.1016/j.molcel.2009.06.009

    Figure Lengend Snippet: Elongation Complex Footprint and Mapping of the Transcription Bubble (A) (Upper) Summary of elongation complex preparation, drawn to scale. (Lower) Elongation complexes with 5′ end-labeled, 131-mer transcribed DNA were digested with increasing amounts of DNase I, as indicated. The footprint region where DNase I cleavage is repressed (bold line) and a hypersensitive site (sphere) are indicated on the right. M, thymine-specific cleavage marker. Elongation complex (oval) and RNA (bold line) are indicated on the left. Position of the active site is taken as +1. (B) (Upper) Schematic diagram of the locations of the RNA primer (bold text) and G stop (gray box) in the elongation complex. The 150-mer transcribed strand (TS), the corresponding end-labeled nontranscribed strand (NTS), and the direction of exonuclease digestion are indicated. (Lower) Elongation complexes incubated alone, or with ATP/UTP/GTP and TFIIS, were digested with T7 exonuclease to mark their position(s), modified with increasing amounts of KMnO 4 (2 and 8 mM), and analyzed by denaturing PAGE (lanes 1–4). Bands corresponding to the major elongation complexes (2 mM KMnO 4 experiment shown) were isolated, cleaved at modified thymines with piperidine, and resolved by denaturing PAGE (lanes 5 and 6). DNA sequence is shown on the left. Spheres, modified thymines. Arrowheads, positions of active sites. (C) Crystal structure of the elongation complex with modeled DNA paths (dashed lines). Space-filling model shows the DNA (color) engulfed in protein bulk. (D) Area protected by RNAPII (DNase I footprinting, solid line; crystallography model, dashed line) and their transcription bubbles. Only reconstituted elongation complex was mapped by DNase I footprinting. However, T7 exonuclease digests to the same distance from the edge of the two footprints (±1 base; positions indicated by vertical arrow) before and after transcription, showing that RNAPII moved forward upon NTP addition.

    Article Snippet: T7 exonuclease footprinting: radioactively end-labeled ECs were incubated with 0.4 units/μl T7 exonuclease (NEB) at 26°C.

    Techniques: Labeling, Marker, Incubation, Modification, Polyacrylamide Gel Electrophoresis, Isolation, Sequencing, Footprinting

    T7 exonuclease digestion to determine the topology of end-joined products. A , diagrammatic representation of plausible end joined products by cell-free extracts. B , T7 exonuclease and XhoI digestion followed by T7 exonuclease digestion pattern of end-joined products of K562 cell-free extracts. Multiple end-joining reactions were carried out using 5′ compatible substrates, and products were incubated with either T7 exonuclease (5 units/10-μl reaction for 2 h), XhoI, or both. The products were resolved on an 8% denaturing PAGE. M , 50-nt ladder.

    Journal: The Journal of Biological Chemistry

    Article Title: Anti-apoptotic Protein BCL2 Down-regulates DNA End Joining in Cancer Cells *

    doi: 10.1074/jbc.M110.140350

    Figure Lengend Snippet: T7 exonuclease digestion to determine the topology of end-joined products. A , diagrammatic representation of plausible end joined products by cell-free extracts. B , T7 exonuclease and XhoI digestion followed by T7 exonuclease digestion pattern of end-joined products of K562 cell-free extracts. Multiple end-joining reactions were carried out using 5′ compatible substrates, and products were incubated with either T7 exonuclease (5 units/10-μl reaction for 2 h), XhoI, or both. The products were resolved on an 8% denaturing PAGE. M , 50-nt ladder.

    Article Snippet: T7 exonuclease digestion was performed by incubating purified EJ products with either increasing concentrations or 5 units of T7 exonuclease (New England Biolabs) at 25 °C for 2 h. In some cases, a fraction of EJ products was digested with XhoI (4 units) (37 °C for 4 h) prior to T7 exonuclease digestion.

    Techniques: Incubation, Polyacrylamide Gel Electrophoresis

    Different RecE/RecT and Redα/Redβ recombination mechanisms revealed by different substrates. ( A ) Relative recombination efficiencies achieved using RecE/RecT (ET) or Redα/Redβ (βα) expression constructs in either JC5547 or JC5519 as indicated, as a function of homology region length, are shown. Linear molecules, which were generated to contain homology regions of variable length at their ends, were allowed to recombine with a prelinearized target generated by restriction digestion. Recombination efficiencies from one experiment are shown relative to the maximum recombination efficiency of  B , which was set to 1. Recombination efficiencies are thus presented as relative and are not directly comparable to those shown in previous figures. The experiment was repeated twice, producing similar results. (█) 5547ET; (○) 5519ET; (●) 5547βα; (□) 5519βα. ( B ) Same as  A , except that the target was left intact. The maximum absolute recombination efficiency found was arbitrarily set to 1, and all other recombination efficiencies were related to this maximum. Recombination efficiencies from one experiment are shown. The experiment was repeated five times, producing similar results. The experiments shown in  A  and  B  were done in parallel with the same batches of competent cells and PCR fragments. Colony numbers observed in these experiments were adjusted to relative recombination efficiencies by relating to the maximums obtained in  B , which were set to 1. (█) 5547ET; (○) 5519ET; (●) 5547βα; (□) 5519βα. ( C ) Recombination efficiencies in the presence of the indicated expression constructs in JC5519 using two linear molecules, both of which were preresected in vitro using T7 gene six exonuclease. Data from one representative experiment is shown, in which pools of preresected molecules (which shared 400 nucleotide homology regions and were generated using six different incubation conditions with T7 gene 6 exonuclease) were recombined. C, no exogenous protein expressed; β, expression of Redβ only; βα, coexpression of Redβ and Redα; T, expression of RecT only; ET, coexpression of RecE and RecT. Recombination efficiencies are shown relative to the maximum of  B .

    Journal: Genes & Development

    Article Title: RecE/RecT and Red?/Red? initiate double-stranded break repair by specifically interacting with their respective partners

    doi:

    Figure Lengend Snippet: Different RecE/RecT and Redα/Redβ recombination mechanisms revealed by different substrates. ( A ) Relative recombination efficiencies achieved using RecE/RecT (ET) or Redα/Redβ (βα) expression constructs in either JC5547 or JC5519 as indicated, as a function of homology region length, are shown. Linear molecules, which were generated to contain homology regions of variable length at their ends, were allowed to recombine with a prelinearized target generated by restriction digestion. Recombination efficiencies from one experiment are shown relative to the maximum recombination efficiency of B , which was set to 1. Recombination efficiencies are thus presented as relative and are not directly comparable to those shown in previous figures. The experiment was repeated twice, producing similar results. (█) 5547ET; (○) 5519ET; (●) 5547βα; (□) 5519βα. ( B ) Same as A , except that the target was left intact. The maximum absolute recombination efficiency found was arbitrarily set to 1, and all other recombination efficiencies were related to this maximum. Recombination efficiencies from one experiment are shown. The experiment was repeated five times, producing similar results. The experiments shown in A and B were done in parallel with the same batches of competent cells and PCR fragments. Colony numbers observed in these experiments were adjusted to relative recombination efficiencies by relating to the maximums obtained in B , which were set to 1. (█) 5547ET; (○) 5519ET; (●) 5547βα; (□) 5519βα. ( C ) Recombination efficiencies in the presence of the indicated expression constructs in JC5519 using two linear molecules, both of which were preresected in vitro using T7 gene six exonuclease. Data from one representative experiment is shown, in which pools of preresected molecules (which shared 400 nucleotide homology regions and were generated using six different incubation conditions with T7 gene 6 exonuclease) were recombined. C, no exogenous protein expressed; β, expression of Redβ only; βα, coexpression of Redβ and Redα; T, expression of RecT only; ET, coexpression of RecE and RecT. Recombination efficiencies are shown relative to the maximum of B .

    Article Snippet: T7 gene 6 exonuclease digestion was done in the buffer provided by the supplier (Amersham, Inc.), using ∼1.5 μg linear substrate per reaction.

    Techniques: Expressing, Construct, Generated, Polymerase Chain Reaction, In Vitro, Incubation

    Validation of the overhang protection assay. (A) The overhang protection assay was performed on single-stranded oligonucleotides containing (TTAGGG) n repeats ( n = 6, 9, 16, 32, 48, and 64). Oligonucleotides were either annealed directly to the C-rich probe (annealed) or underwent the overhang protection assay (protected). Weighted mean sizes were calculated after quantitating the signals in each lane with ImageQuant software between molecular size (M) marker positions of 36 to 384 bp. (B) Results of the assay in panel A are plotted. (C) The overhang protection assay was performed on the model template pBSK-Rep4, which contained an ∼450-nt 3′ (TTAGGG) n overhang after 3 kb of double-stranded pBSK vector sequences. Prior to the assay, a different amount of pBSK-Rep4 was mixed with or without HeLa genomic DNA. (D) Whole genomic DNA from HeLa cells was digested with T7 gene 6 exonuclease (a 5′-to-3′ exonuclease) for the indicated times and then treated with or without Exo I before being analyzed in the overhang protection assay. Black lines indicate positions of the bulk of the overhang DNA.

    Journal: Molecular and Cellular Biology

    Article Title: Human Telomeres Maintain Their Overhang Length at Senescence †

    doi: 10.1128/MCB.25.6.2158-2168.2005

    Figure Lengend Snippet: Validation of the overhang protection assay. (A) The overhang protection assay was performed on single-stranded oligonucleotides containing (TTAGGG) n repeats ( n = 6, 9, 16, 32, 48, and 64). Oligonucleotides were either annealed directly to the C-rich probe (annealed) or underwent the overhang protection assay (protected). Weighted mean sizes were calculated after quantitating the signals in each lane with ImageQuant software between molecular size (M) marker positions of 36 to 384 bp. (B) Results of the assay in panel A are plotted. (C) The overhang protection assay was performed on the model template pBSK-Rep4, which contained an ∼450-nt 3′ (TTAGGG) n overhang after 3 kb of double-stranded pBSK vector sequences. Prior to the assay, a different amount of pBSK-Rep4 was mixed with or without HeLa genomic DNA. (D) Whole genomic DNA from HeLa cells was digested with T7 gene 6 exonuclease (a 5′-to-3′ exonuclease) for the indicated times and then treated with or without Exo I before being analyzed in the overhang protection assay. Black lines indicate positions of the bulk of the overhang DNA.

    Article Snippet: To generate longer 3′ overhangs, total DNA was treated with the 5′-to-3′ T7 gene 6 exonuclease (2 U/μg of DNA; Amersham) in 40 mM Tris-HCl (pH 7.5)-20 mM MgCl2 -50 mM NaCl at 37°C for the indicated times and stopped with 25 mM EDTA (pH 8.0).

    Techniques: Software, Marker, Plasmid Preparation

    Dual biotin-labeled DNA fragments form a closed substrate on the surface of the BLI probe. (A) A schematic of a double digestion assay using Exonuclease T7 + Exonuclease VII and PCR. PCR was performed using M13F, M13R oligos, and DNA attached to the BLI surface as a template. (B) The BLI probe was severed from the plastic adaptor and immerged into a PCR master mix. (C) Dual biotin-labeled DNA fragments on the BLI surface were resistant to Exo T7 + Exo VII digestion while single biotin-labeled DNA fragments on the BLI surface were not.

    Journal: bioRxiv

    Article Title: ParB spreading on DNA requires cytidine triphosphate in vitro

    doi: 10.1101/2019.12.11.865972

    Figure Lengend Snippet: Dual biotin-labeled DNA fragments form a closed substrate on the surface of the BLI probe. (A) A schematic of a double digestion assay using Exonuclease T7 + Exonuclease VII and PCR. PCR was performed using M13F, M13R oligos, and DNA attached to the BLI surface as a template. (B) The BLI probe was severed from the plastic adaptor and immerged into a PCR master mix. (C) Dual biotin-labeled DNA fragments on the BLI surface were resistant to Exo T7 + Exo VII digestion while single biotin-labeled DNA fragments on the BLI surface were not.

    Article Snippet: To verify that dual biotin-labeled DNA fragments formed a closed substrate on the surface of the BLI probe, we performed a double digestion with Exonuclease T7 and Exonuclease VII (NEB) ( ).

    Techniques: Labeling, Polymerase Chain Reaction