escherichia coli exonuclease  (New England Biolabs)


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    New England Biolabs escherichia coli exonuclease
    Escherichia Coli Exonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 88/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/escherichia coli exonuclease/product/New England Biolabs
    Average 88 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    escherichia coli exonuclease - by Bioz Stars, 2020-02
    88/100 stars

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    Related Articles

    Electron Microscopy:

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Coverglass (no. 15) was purchased either as 22 × 30 mm coverslips from VWR (48393–150) or as 50-well chambers from Electron Microscopy Sciences (70460–50R). .. Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs.

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Coverglass (no. 15) was purchased either as 22 × 30 mm coverslips from VWR (48393–150) or as 50-well chambers from Electron Microscopy Sciences (70460–50R). .. Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs.

    Amplification:

    Article Title: Is Bocourt's Terrific Skink Really So Terrific? Trophic Myth and Reality
    Article Snippet: The following primers were used: 12S rDNA: 12SA 5´-AAACTGGGATTAGATACCCCACTAT-3´ and 12SB 5´-GAGGGTGACGGGCGGTGTGT-3´ [ ] amplified a ~400 base pair fragment while 16S rDNA 5´-GCCTGTTTATCAAAAACAT-3´ and 16SH 5´-CCGGTCTGAACTCAGATCACGT- 3´ [ ] amplified a ~700 base pair fragment. .. Excess primers and dNTPs were removed from the PCR product using an enzymatic reaction; Escherichia coli exonuclease I, Antartic phosphatase, and Antartic phosphatase buffer (all New England Biolabs) were added to each sample.

    Article Title: Treerunners, cryptic lizards of the Plica plica group (Squamata, Sauria, Tropiduridae) of northern South America
    Article Snippet: Following the PCR, excess primers and dNTPs were removed using enzymatic reaction of Escherichia coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs). .. The primers for the12S rDNA: 12SA 5´- AAACTGGGATTAGATACCCCACTAT- 3´, 12SB 5´- GAGGGTGACGGGCGGTGTGT-3´ and 16S rDNA: 5´- GCCTGTTTATCAAAAACAT-3´, 16SH 5´- CCGGTCTGAACTCAGATCACGT- 3´ amplified approximately a 400 and 500 respectively base pair fraction (Genbank accessions: 12S rDNA; KU 895880, 16S rDNA; KU 895881).

    Agarose Gel Electrophoresis:

    Article Title: Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae
    Article Snippet: Native and denatured southern blotting Genomic DNA from non-synchronised saturated cell cultures was digested overnight with XhoI (Takara, 1094A) and then separated on 1% agarose gel (15 cm in length) for 18 hours at 25 volts. .. E. coli exonuclease I digestion (New England biolabs, M0293S) was performed prior to XhoI digestion of the genomic DNA.

    In Vitro:

    Article Title: RAD50 Is Required for Efficient Initiation of Resection and Recombinational Repair at Random, ?-Induced Double-Strand Break Ends
    Article Snippet: .. Digestion of in vitro resected (λ exonuclease treated) λ DNA with E. coli exonuclease I to remove single strand 3′ tails Plugs of resected λ DNA (∼50 µl volume) were equilibrated in 500 µl of TE (10 mM Tris, pH 8.0, 1 mM EDTA), and then incubated in 200 µl of 1.25× reaction buffer (supplied by NEB) with 100 units of exonuclease I at 37°C for 30 minutes. .. Immediately after the exonuclease I incubation, plugs were transferred to 1 ml 100 mM EDTA containing 1 mg/ml proteinase K and 1% sarcosyl and incubated for 2 hours at 37°C.

    Southern Blot:

    Article Title: Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae
    Article Snippet: Paragraph title: Native and denatured southern blotting ... E. coli exonuclease I digestion (New England biolabs, M0293S) was performed prior to XhoI digestion of the genomic DNA.

    Polymerase Chain Reaction:

    Article Title: Social and Population Structure in the Ant Cataglyphis emmae
    Article Snippet: .. Following the PCR reactions, excess primers and dNTPs were removed using enzymatic reaction of E. coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs). .. Sequencing was carried out in both directions using the BigDye® Terminator v1.1 cycle sequencing kit (Applied Biosystems) according to the manufacturer’s instructions.

    Article Title: Is Bocourt's Terrific Skink Really So Terrific? Trophic Myth and Reality
    Article Snippet: .. Excess primers and dNTPs were removed from the PCR product using an enzymatic reaction; Escherichia coli exonuclease I, Antartic phosphatase, and Antartic phosphatase buffer (all New England Biolabs) were added to each sample. .. Sequencing was carried out in both directions using the BigDye® Terminator v1.1 cycle sequencing kit (Applied Biosystems) in accordance with the manufacturer's instructions.

    Article Title: Treerunners, cryptic lizards of the Plica plica group (Squamata, Sauria, Tropiduridae) of northern South America
    Article Snippet: .. Following the PCR, excess primers and dNTPs were removed using enzymatic reaction of Escherichia coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs). .. Sequencing was carried out in both directions using the BigDye® Terminator v1.1 cycle sequencing kit (Applied Biosystems) according to the manufacturer’s instructions.

    Lambda DNA Preparation:

    Article Title: RAD50 Is Required for Efficient Initiation of Resection and Recombinational Repair at Random, ?-Induced Double-Strand Break Ends
    Article Snippet: .. Enzymatic treatments of lambda DNA Bacteriophage λ DNA, λ-exonuclease, and E. coli exonuclease I were purchased from New England Biolabs (NEB, Beverly, MA) and were used with supplied buffers according to manufacturer's instructions. .. In vitro resection of λ DNA with λ exonuclease λ DNA was digested at 37°C at a final concentration of 20 µg/ml DNA and 147 units/ml of λ-exonuclease.

    Avidin-Biotin Assay:

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Avidin-labeled Quantum Dot 605 nm (Q10103MP) and FluoSpheres (F8770) were purchased from ThermoFisher Scientific. .. Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs.

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Avidin-labeled Quantum Dot 605 nm (Q10103MP) and FluoSpheres (F8770) were purchased from ThermoFisher Scientific. .. Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs.

    Labeling:

    Article Title: Is Bocourt's Terrific Skink Really So Terrific? Trophic Myth and Reality
    Article Snippet: Excess primers and dNTPs were removed from the PCR product using an enzymatic reaction; Escherichia coli exonuclease I, Antartic phosphatase, and Antartic phosphatase buffer (all New England Biolabs) were added to each sample. .. Labeled fragments were resolved on an automated A3130xl genetic analyzer (Applied Biosystems).

    Purification:

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs. .. DNA or RNA oligonucleotides (oligos) with sequences shown in were purchased from Integrated DNA Technologies and purified by polyacrylamide gel electrophoresis; some oligos were modified with 5′-dibenzylcyclooctyne (DBCO) with tetraethylene glycol spacer (/5DBCOTEG/) or 5′-phosphate (5APhos).

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs. .. DNA or RNA oligonucleotides (oligos) with sequences shown in were purchased from Integrated DNA Technologies and purified by polyacrylamide gel electrophoresis; some oligos were modified with 5′-dibenzylcyclooctyne (DBCO) with tetraethylene glycol spacer (/5DBCOTEG/) or 5′-phosphate (5APhos).

    SYBR Green Assay:

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Sodium hydroxide ( > 97%), glacial acetic acid ( > 99.7%), sodium bicarbonate ( > 99.7%), tris(hydroxymethyl)-aminomethane (Tris base), Tween 20, ethylenediaminetetraacetic acid (EDTA), biotin-dUTP (40029), SYBR Green I nucleic acid gel stain (SYBR Green), and SYBR Gold nucleic acid gel stain (SYBR Gold) were also purchased from ThermoFisher Scientific. .. Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs.

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Sodium hydroxide ( > 97%), glacial acetic acid ( > 99.7%), sodium bicarbonate ( > 99.7%), tris(hydroxymethyl)-aminomethane (Tris base), Tween 20, ethylenediaminetetraacetic acid (EDTA), biotin-dUTP (40029), SYBR Green I nucleic acid gel stain (SYBR Green), and SYBR Gold nucleic acid gel stain (SYBR Gold) were also purchased from ThermoFisher Scientific. .. Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs.

    Modification:

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs. .. DNA or RNA oligonucleotides (oligos) with sequences shown in were purchased from Integrated DNA Technologies and purified by polyacrylamide gel electrophoresis; some oligos were modified with 5′-dibenzylcyclooctyne (DBCO) with tetraethylene glycol spacer (/5DBCOTEG/) or 5′-phosphate (5APhos).

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs. .. DNA or RNA oligonucleotides (oligos) with sequences shown in were purchased from Integrated DNA Technologies and purified by polyacrylamide gel electrophoresis; some oligos were modified with 5′-dibenzylcyclooctyne (DBCO) with tetraethylene glycol spacer (/5DBCOTEG/) or 5′-phosphate (5APhos).

    Incubation:

    Article Title: Functional Relationship of ATP Hydrolysis, Presynaptic Filament Stability, and Homologous DNA Pairing Activity of the Human Meiotic Recombinase DMC1 *
    Article Snippet: .. For this assay, His6 -tagged DMC1 or DMC1 D317K was incubated with either 5′ or 3′ 32 P-labeled Oligo 1 ssDNA (3 μ m nucleotides) in 9 μl of buffer B (35 m m Tris-HCl, pH 7.5, 1 m m DTT, 100 ng/μl BSA, 100 m m KCl and 5 m m MgCl2 ) with 1 m m nucleotide (ATP, AMP-PNP, or AMP-PCP, as indicated) at 37 °C for 5 min. Then, E. coli Exonuclease I, which has a 3′ to 5′ polarity and was used to test the 5′ end-labeled DNA (0.8 unit; New England Biolabs), or E. coli RecJ, which has a 5′ to 3′ polarity and was used to test the 3′ end-labeled DNA, was added to the reaction mixture (10 μl final volume). .. After 5 min of digestion at 37 °C, reaction mixtures were mixed with 2.5 μl of termination buffer (240 m m EDTA, 0.2% SDS, and proteinase K at 0.32 mg/ml) and incubated at 37 °C for 15 min. Then, the reaction mixtures were resolved in a 10% polyacrylamide gel in TBE buffer (89 m m Tris, 89 m m borate, and 2 m m EDTA, pH 8.0), and after drying the gel, the DNA species were quantified by phosphorimaging analysis.

    Article Title: RAD50 Is Required for Efficient Initiation of Resection and Recombinational Repair at Random, ?-Induced Double-Strand Break Ends
    Article Snippet: .. Digestion of in vitro resected (λ exonuclease treated) λ DNA with E. coli exonuclease I to remove single strand 3′ tails Plugs of resected λ DNA (∼50 µl volume) were equilibrated in 500 µl of TE (10 mM Tris, pH 8.0, 1 mM EDTA), and then incubated in 200 µl of 1.25× reaction buffer (supplied by NEB) with 100 units of exonuclease I at 37°C for 30 minutes. .. Immediately after the exonuclease I incubation, plugs were transferred to 1 ml 100 mM EDTA containing 1 mg/ml proteinase K and 1% sarcosyl and incubated for 2 hours at 37°C.

    other:

    Article Title: Construction of a circular single-stranded DNA template containing a defined lesion
    Article Snippet: E.coli DNA polymerase I (Klenow Fragment) [pol I (Kf)], E.coli Exonuclease III, E.coli Exonuclease I, E.coli Uracil DNA glycosylase, E.coli RecA, T7 DNA polymerase, T4 Polynucleotide kinase, and M13KO7 helper phage were all purchased from New England Biolabs (Ipswich, MA).

    Polyacrylamide Gel Electrophoresis:

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs. .. DNA or RNA oligonucleotides (oligos) with sequences shown in were purchased from Integrated DNA Technologies and purified by polyacrylamide gel electrophoresis; some oligos were modified with 5′-dibenzylcyclooctyne (DBCO) with tetraethylene glycol spacer (/5DBCOTEG/) or 5′-phosphate (5APhos).

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs. .. DNA or RNA oligonucleotides (oligos) with sequences shown in were purchased from Integrated DNA Technologies and purified by polyacrylamide gel electrophoresis; some oligos were modified with 5′-dibenzylcyclooctyne (DBCO) with tetraethylene glycol spacer (/5DBCOTEG/) or 5′-phosphate (5APhos).

    Sequencing:

    Article Title: Social and Population Structure in the Ant Cataglyphis emmae
    Article Snippet: Following the PCR reactions, excess primers and dNTPs were removed using enzymatic reaction of E. coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs). .. Sequencing was carried out in both directions using the BigDye® Terminator v1.1 cycle sequencing kit (Applied Biosystems) according to the manufacturer’s instructions.

    Article Title: Is Bocourt's Terrific Skink Really So Terrific? Trophic Myth and Reality
    Article Snippet: Excess primers and dNTPs were removed from the PCR product using an enzymatic reaction; Escherichia coli exonuclease I, Antartic phosphatase, and Antartic phosphatase buffer (all New England Biolabs) were added to each sample. .. Sequencing was carried out in both directions using the BigDye® Terminator v1.1 cycle sequencing kit (Applied Biosystems) in accordance with the manufacturer's instructions.

    Article Title: Treerunners, cryptic lizards of the Plica plica group (Squamata, Sauria, Tropiduridae) of northern South America
    Article Snippet: Following the PCR, excess primers and dNTPs were removed using enzymatic reaction of Escherichia coli Exonuclease I, Antartic phosphatase and Antartic phosphatase buffer (all New England Biolabs). .. Sequencing was carried out in both directions using the BigDye® Terminator v1.1 cycle sequencing kit (Applied Biosystems) according to the manufacturer’s instructions.

    Staining:

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Sodium hydroxide ( > 97%), glacial acetic acid ( > 99.7%), sodium bicarbonate ( > 99.7%), tris(hydroxymethyl)-aminomethane (Tris base), Tween 20, ethylenediaminetetraacetic acid (EDTA), biotin-dUTP (40029), SYBR Green I nucleic acid gel stain (SYBR Green), and SYBR Gold nucleic acid gel stain (SYBR Gold) were also purchased from ThermoFisher Scientific. .. Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs.

    Article Title: Expanding the Dynamic Range of Fluorescence Assays through Single-Molecule Counting and Intensity Calibration
    Article Snippet: Sodium hydroxide ( > 97%), glacial acetic acid ( > 99.7%), sodium bicarbonate ( > 99.7%), tris(hydroxymethyl)-aminomethane (Tris base), Tween 20, ethylenediaminetetraacetic acid (EDTA), biotin-dUTP (40029), SYBR Green I nucleic acid gel stain (SYBR Green), and SYBR Gold nucleic acid gel stain (SYBR Gold) were also purchased from ThermoFisher Scientific. .. Deoxy-nucleotide solution mix (dNTP), phi29 DNA polymerase (Φ29 polymerase), and Escherichia coli exonuclease I were purchased from New England Biolabs.

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    New England Biolabs exonuclease iii
    Probing of the EC translocation conformations. ( A ) <t>Exo</t> <t>III</t> footprints of EC14 and EC15. Tth EC14 (lanes 1 and 2) was assembled as described in Materials and Methods. EC15 (lanes 3 and 4) was obtained by incubation of EC14 with substrate ATP for 2 min at 60°C. Exo III (0.02 U/μl) was added for 5 (lanes 1 and 3) or 10 (lanes 2 and 4) min at 37°C. ( B ) Schematics of RNAP front edge oscillations in EC14 and EC15. ( C ) Photo cross-linking patterns of Tth EC14 and EC15, EC14 and EC15 containing 5′ 32 P-labeled RNA primers were prepared as illustrated (left). The photo cross-linking analog 4-thio UTP (50 μM) was incorporated into the transcript for 2 min at 60°C followed UV light irradiation for 5 min at RT. The cross-linked species were separated using gel electrophoresis (right).
    Exonuclease Iii, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 95/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/exonuclease iii/product/New England Biolabs
    Average 95 stars, based on 5 article reviews
    Price from $9.99 to $1999.99
    exonuclease iii - by Bioz Stars, 2020-02
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    Probing of the EC translocation conformations. ( A ) Exo III footprints of EC14 and EC15. Tth EC14 (lanes 1 and 2) was assembled as described in Materials and Methods. EC15 (lanes 3 and 4) was obtained by incubation of EC14 with substrate ATP for 2 min at 60°C. Exo III (0.02 U/μl) was added for 5 (lanes 1 and 3) or 10 (lanes 2 and 4) min at 37°C. ( B ) Schematics of RNAP front edge oscillations in EC14 and EC15. ( C ) Photo cross-linking patterns of Tth EC14 and EC15, EC14 and EC15 containing 5′ 32 P-labeled RNA primers were prepared as illustrated (left). The photo cross-linking analog 4-thio UTP (50 μM) was incorporated into the transcript for 2 min at 60°C followed UV light irradiation for 5 min at RT. The cross-linked species were separated using gel electrophoresis (right).

    Journal: Nucleic Acids Research

    Article Title: Elongation complexes of Thermus thermophilus RNA polymerase that possess distinct translocation conformations

    doi: 10.1093/nar/gkl559

    Figure Lengend Snippet: Probing of the EC translocation conformations. ( A ) Exo III footprints of EC14 and EC15. Tth EC14 (lanes 1 and 2) was assembled as described in Materials and Methods. EC15 (lanes 3 and 4) was obtained by incubation of EC14 with substrate ATP for 2 min at 60°C. Exo III (0.02 U/μl) was added for 5 (lanes 1 and 3) or 10 (lanes 2 and 4) min at 37°C. ( B ) Schematics of RNAP front edge oscillations in EC14 and EC15. ( C ) Photo cross-linking patterns of Tth EC14 and EC15, EC14 and EC15 containing 5′ 32 P-labeled RNA primers were prepared as illustrated (left). The photo cross-linking analog 4-thio UTP (50 μM) was incorporated into the transcript for 2 min at 60°C followed UV light irradiation for 5 min at RT. The cross-linked species were separated using gel electrophoresis (right).

    Article Snippet: Exonuclease III (Exo III) (NEB, 0.1 U/μl) was added for 5–10 min at 37°C.

    Techniques: Translocation Assay, Incubation, Labeling, Irradiation, Nucleic Acid Electrophoresis

    Chromatographic separation of 3′-5′ exodeoxyribonuclease activity associated with preparations of Exonuclease IX. ( A ) SDS–PAGE analysis of the purification of ExoIX from cell lysate of induced BL21 (pJONEX/ xni , pcI857). SPL, cleared cell lysate applied to SP/first Heparin column (28 µg); QL, Q load (6 µg); H2L, second Heparin column load (5 µg); IX, concentrated ExoIX eluate from second Heparin (7.5 µg). (B–D). Eluted fractions from first Heparin column were separated by SDS–PAGE. ( B ) Ethidium bromide stained substrate gel. High molecular weight DNA cast in the gel fluoresces with UV, while regions of DNA degradation appear as darker bands. Early fractions (lanes 1–4), contain detectable exonuclease activity. ( C ) The same gel counter-stained with Coomassie G250. Over-expressed ExoIX is eluted in later fractions (lanes 5 and 6). ( D ) Superimposition of images in panels B and C, demonstrating that exonuclease activity can be resolved from ExoIX. A fraction represented in lane 4 was used for subsequent enrichment and identification of the co-purifying nuclease. Lanes, 1–6, heparin fractions (2.5 µl); 7, loading sample (5 µl); 8, flow through (5 µl). ( E ) Highly purified ExoIX lacks activity on a single-stranded DNA substrate (34-mer). Protein samples taken during the purification of ExoIX were incubated with 15 fmol 32 P-labelled 34-mer at 37°C for 10 min in the presence of 10 mM MgCl 2 and the reaction products separated by denaturing PAGE. Reactions (10 µl) contained varying amounts of protein. SPL, 0.7 and 0.07 µg of protein from cell-free extract of induced cells expressing ExoIX; QL, 0.1 and 0.01 µg of protein loaded on to first anion exchange column; H2L, 3 and 0.3 µg of protein from sample loaded onto second heparin column; IX, contains samples from final purified fraction of ExoIX eluted from second heparin column, 5 and 0.5 µg; two positive controls are also shown, bacteriophage T5 D15 exonuclease (T5), 0.1 and 0.01 µg and exonuclease III (III), 0.03 and 0.003 µg.

    Journal: Nucleic Acids Research

    Article Title: Molecular interactions of Escherichia coli ExoIX and identification of its associated 3?-5? exonuclease activity

    doi: 10.1093/nar/gkm396

    Figure Lengend Snippet: Chromatographic separation of 3′-5′ exodeoxyribonuclease activity associated with preparations of Exonuclease IX. ( A ) SDS–PAGE analysis of the purification of ExoIX from cell lysate of induced BL21 (pJONEX/ xni , pcI857). SPL, cleared cell lysate applied to SP/first Heparin column (28 µg); QL, Q load (6 µg); H2L, second Heparin column load (5 µg); IX, concentrated ExoIX eluate from second Heparin (7.5 µg). (B–D). Eluted fractions from first Heparin column were separated by SDS–PAGE. ( B ) Ethidium bromide stained substrate gel. High molecular weight DNA cast in the gel fluoresces with UV, while regions of DNA degradation appear as darker bands. Early fractions (lanes 1–4), contain detectable exonuclease activity. ( C ) The same gel counter-stained with Coomassie G250. Over-expressed ExoIX is eluted in later fractions (lanes 5 and 6). ( D ) Superimposition of images in panels B and C, demonstrating that exonuclease activity can be resolved from ExoIX. A fraction represented in lane 4 was used for subsequent enrichment and identification of the co-purifying nuclease. Lanes, 1–6, heparin fractions (2.5 µl); 7, loading sample (5 µl); 8, flow through (5 µl). ( E ) Highly purified ExoIX lacks activity on a single-stranded DNA substrate (34-mer). Protein samples taken during the purification of ExoIX were incubated with 15 fmol 32 P-labelled 34-mer at 37°C for 10 min in the presence of 10 mM MgCl 2 and the reaction products separated by denaturing PAGE. Reactions (10 µl) contained varying amounts of protein. SPL, 0.7 and 0.07 µg of protein from cell-free extract of induced cells expressing ExoIX; QL, 0.1 and 0.01 µg of protein loaded on to first anion exchange column; H2L, 3 and 0.3 µg of protein from sample loaded onto second heparin column; IX, contains samples from final purified fraction of ExoIX eluted from second heparin column, 5 and 0.5 µg; two positive controls are also shown, bacteriophage T5 D15 exonuclease (T5), 0.1 and 0.01 µg and exonuclease III (III), 0.03 and 0.003 µg.

    Article Snippet: Two positive controls, T5 D15 5′-3′ exonuclease ( ) and exonuclease III (New England Biolabs) were also included in the assays.

    Techniques: Activity Assay, SDS Page, Purification, Staining, Molecular Weight, Flow Cytometry, Incubation, Polyacrylamide Gel Electrophoresis, Expressing

    Sequences of pKMP2 plasmids treated with AID during transcription and amplified in E. coli in the presence of ampicillin. The WT sequence is shown on the top lines. The two MP2 nucleosome positioning sequences are in green (BamHI sites underlined). The in-frame ACG initiation codons are in italics and underlined. The in-frame stop codons are underlined and not italicized. The AID-created Ts resulting in a potential TATA box present in all 35 clones are in bold font. The Shine-Dalgarno sequence (AGGAAG) is in blue. The transcription start site of unmutated pKMP2 plasmids in E. coli is in purple and underlined. The 5′ end of the Amp r coding region is in red. The ACG start codon for Amp r is at 3041–3043. Dashed lines represent agreement with the unmutated pKMP2 with mutations indicated by lowercase font. The sequences were obtained from one of three experiments.

    Journal: The Journal of Experimental Medicine

    Article Title: The activation-induced cytidine deaminase (AID) efficiently targets DNA in nucleosomes but only during transcription

    doi: 10.1084/jem.20082678

    Figure Lengend Snippet: Sequences of pKMP2 plasmids treated with AID during transcription and amplified in E. coli in the presence of ampicillin. The WT sequence is shown on the top lines. The two MP2 nucleosome positioning sequences are in green (BamHI sites underlined). The in-frame ACG initiation codons are in italics and underlined. The in-frame stop codons are underlined and not italicized. The AID-created Ts resulting in a potential TATA box present in all 35 clones are in bold font. The Shine-Dalgarno sequence (AGGAAG) is in blue. The transcription start site of unmutated pKMP2 plasmids in E. coli is in purple and underlined. The 5′ end of the Amp r coding region is in red. The ACG start codon for Amp r is at 3041–3043. Dashed lines represent agreement with the unmutated pKMP2 with mutations indicated by lowercase font. The sequences were obtained from one of three experiments.

    Article Snippet: Reactions were performed with 20 nM of sucrose gradient–purified nucleosomes and 30 U exonuclease III (New England Biolabs, Inc.) in buffer 1 (New England Biolabs, Inc.).

    Techniques: Amplification, Sequencing, Clone Assay

    Enzymatic resistance of phosphorothioate-modified Au-TDNNs. (A, B) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by DNase I. (C, D) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by Exo III.

    Journal: Theranostics

    Article Title: High-Discrimination Factor Nanosensor Based on Tetrahedral DNA Nanostructures and Gold Nanoparticles for Detection of MiRNA-21 in Live Cells

    doi: 10.7150/thno.23852

    Figure Lengend Snippet: Enzymatic resistance of phosphorothioate-modified Au-TDNNs. (A, B) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by DNase I. (C, D) Fluorescence time graph depicting terminal-modified Au-TDNN and overall-modified Au-TDNN degradation by Exo III.

    Article Snippet: For both human DNase I (Thermo Scientific) and exonuclease III (New England Biolabs) digestion, a common concentration of 3 U/mL was used to digest 2 nM Au-TDNNs samples in PBS.

    Techniques: Modification, Fluorescence